From eaebb8513e44ba04c1c3c612d56f48f21cb97d82 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Tue, 14 Jul 2026 15:57:19 -0400 Subject: [PATCH 1/8] docs: track CL term corrections in reports and ROADMAP Add reports/cl_term_issues.md to document proposed CL label/definition changes identified during SOULCAP mapping (issue #13: CL:4052055 -> CD56-positive T cell, CL:0000814 -> iNKT cell). Link from ROADMAP.md CL corrections table. Co-Authored-By: Claude Sonnet 4.6 --- ROADMAP.md | 13 +++++++++ reports/cl_term_issues.md | 60 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 reports/cl_term_issues.md diff --git a/ROADMAP.md b/ROADMAP.md index 713508d..ea0ea0b 100644 --- a/ROADMAP.md +++ b/ROADMAP.md @@ -122,6 +122,19 @@ type, proposed CL term + ID, match type (broad/exact), rationale, and the marker --- +## CL term corrections + +Issues discovered during mapping where CL itself needs updating. Tracked in +[reports/cl_term_issues.md](reports/cl_term_issues.md) and as GitHub issues on +this repo (labelled `cl-correction`). Each entry should eventually be filed +upstream to `obophenotype/cell-ontology`. + +| Issue | Terms | Status | +|-------|-------|--------| +| [#13 NKT cell naming](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/13) | CL:4052055 → "CD56-positive T cell, human"; CL:0000814 → "iNKT cell" | Open — not yet filed upstream | + +--- + ## Cross-cutting dependencies - **Marker parser/validator.** Milestones 1, 3, and 4 all need a parser built diff --git a/reports/cl_term_issues.md b/reports/cl_term_issues.md new file mode 100644 index 0000000..b992d28 --- /dev/null +++ b/reports/cl_term_issues.md @@ -0,0 +1,60 @@ +# CL Term Issues + +Proposed corrections and additions to the Cell Ontology (CL) identified during +SOULCAP ↔ CL mapping work. Each entry links to the tracking issue in this repo +and (where filed) to the upstream CL GitHub issue. + +See [CLAUDE.md](../CLAUDE.md) for project conventions. + +--- + +## Open issues + +### NKT cell naming — CL:4052055 and CL:0000814 + +**Repo issue:** [#13 NKT cell naming](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/13) +**Filed by:** Kelly Lundsten · 2026-07-08 +**Reference:** [PMC6647187](https://pmc.ncbi.nlm.nih.gov/articles/PMC6647187/) +**Status:** Open — not yet filed upstream to `obophenotype/cell-ontology` + +#### CL:4052055 — "Mature NK T cell, human" + +| Field | Current | Proposed | +|-------|---------|----------| +| Label | Mature NK T cell, human | CD56-positive T cell, human | +| Definition | "A mature NK T cell that can be identified by the expression of CD56 in humans." | A mature T cell expressing CD56 in humans. | + +**Rationale:** CD56 expression alone defines a CD56-positive T cell, not an NKT +cell. The NKT lineage requires CD1d restriction and an invariant (or semi-invariant) +TCR — neither of which is implied by CD56 expression. Classifying CD56+ T cells +as NKT conflates two distinct populations. + +#### CL:0000814 — "Mature NK T cell" + +| Field | Current | Proposed | +|-------|---------|----------| +| Label | Mature NK T cell | iNKT cell | +| Synonyms | Mature NKT cell; Mature natural killer T cell; … | invariant natural killer T cell; invariant NKT cell; Type I NKT cell | +| Definition | "A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands." | An invariant NKT cell that is CD3-positive, recognises lipid antigens presented by CD1d, and expresses an invariant TCRα chain (TCRVα24-Jα18 in humans, paired with TCRVβ11). | +| Key markers | — | CD3+, CD1d tetramer+, or CD3+ TCRVα24-Jα18+/TCRVβ11+ | + +**Rationale:** The term "NKT" is no longer used as a single unified category. +The field now distinguishes: +- **iNKT** (invariant NKT, Type I) — invariant TCRα chain, CD1d-restricted; + identified by CD3+ CD1d tetramer+ or CD3+ TCRVα24-Jα18+/TCRVβ11+ +- **vNKT** (variant NKT, Type II) — semi-invariant TCR, diverse repertoire +- **CD56+ T cell** — T cells expressing CD56, not CD1d-restricted + +CL:0000814's definition and associated markers (SOULCAP: CD3+ TCRVα24-Jα18+/ +TCRVβ11+) correspond specifically to the iNKT lineage. Renaming to "iNKT cell" +and scoping the definition accordingly prevents conflation with vNKT and CD56+ T +cells. + +**Upstream action needed:** File issue against `obophenotype/cell-ontology` +requesting label change + definition update for both terms. + +--- + +## Resolved issues + +*(none yet)* From 398667d3696314a26f86f98b106e5f11e090dd33 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Wed, 15 Jul 2026 15:35:21 -0400 Subject: [PATCH 2/8] =?UTF-8?q?feat:=20Milestone=201=20=E2=80=94=20marker?= =?UTF-8?q?=5Fprotein=5Fgene.csv=20mapping=20table?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Adds soulcap-map CLI (marker_map.py) that maps all 75 SOULCAP marker tokens to PR, UniProt, HGNC, and gene identifiers, writing the curated deliverable at marker_mappings/marker_protein_gene.csv. Results: 39 fully resolved (PR+HGNC), 17 gene-only (cytokines, TCR segments), 4 PR-only (CD16/CD198/FceR1a/HLA-DR), 15 unresolved (Ig classes, pan-TCR markers, parsing artifacts, CD1d-a-GalCer/Tetramer). Parsing artifacts (V, delta, gamma, delta1) flagged as data quality issues. Sources: cl_pro_relationships.tsv (36 CD markers), OLS4 PR ontology, Monarch Node Normalizer, HGNC REST API. 287 tests passing, 95% coverage. Co-Authored-By: Claude Sonnet 4.6 --- marker_mappings/marker_protein_gene.csv | 76 ++ marker_mappings/marker_tokens.csv | 76 ++ pyproject.toml | 1 + src/soulcap_cl_mapping/marker_map.py | 968 ++++++++++++++++++++ tests/test_marker_map.py | 1087 +++++++++++++++++++++++ 5 files changed, 2208 insertions(+) create mode 100644 marker_mappings/marker_protein_gene.csv create mode 100644 marker_mappings/marker_tokens.csv create mode 100644 src/soulcap_cl_mapping/marker_map.py create mode 100644 tests/test_marker_map.py diff --git a/marker_mappings/marker_protein_gene.csv b/marker_mappings/marker_protein_gene.csv new file mode 100644 index 0000000..548408f --- /dev/null +++ b/marker_mappings/marker_protein_gene.csv @@ -0,0 +1,76 @@ +marker_token,marker_synonyms,source_columns,pro_id,pro_label,uniprot_id,uniprot_label,gene_symbol,hgnc_id,ncbi_gene_id,mapping_method,confidence,evidence,notes +CCR4,CCR4|CD194,Required phenotypic markers,PR:000001200,C-C chemokine receptor type 4,P51679,C-C chemokine receptor type 4,CCR4,HGNC:1605,,inferred,high,reports/cl_pro_relationships.tsv, +CCR6,CCR6|CD196,Required phenotypic markers,PR:000001202,C-C chemokine receptor type 6,P51684,C-C chemokine receptor type 6,CCR6,HGNC:1607,,inferred,high,reports/cl_pro_relationships.tsv, +CD10,,Required phenotypic markers,PR:000001898,neprilysin,P08473,neprilysin,MME,HGNC:7154,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD117,,Required phenotypic markers,PR:000002065,mast/stem cell growth factor receptor,P10721,mast/stem cell growth factor receptor,KIT,HGNC:6342,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD11c,,Ideal exclusion|Required phenotypic markers,PR:000001013,integrin alpha-X,P20702,integrin alpha-X,ITGAX,HGNC:6152,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD123,,Ideal exclusion|Required exclusion|Required phenotypic markers,PR:000001865,interleukin-3 receptor class 2 alpha chain,P26951,interleukin-3 receptor class 2 alpha chain,IL3RA,HGNC:6012,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD127,,Ideal exclusion|Required phenotypic markers,PR:000001869,interleukin-7 receptor subunit alpha,P16871,interleukin-7 receptor subunit alpha,IL7R,HGNC:6024,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD138,,Required phenotypic markers,PR:000001935,syndecan-1,P18827,syndecan-1,SDC1,HGNC:10658,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD14,,Ideal exclusion|Required exclusion|Required phenotypic markers,PR:000001889,CD14 molecule,P08571,CD14 molecule,CD14,HGNC:1628,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD141,,Required phenotypic markers,PR:000002105,thrombomodulin,P07204,thrombomodulin,THBD,HGNC:11784,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD15,,Ideal exclusion|Required exclusion|Required phenotypic markers,PR:000001456,"alpha-(1,3)-fucosyltransferase 4",P22083,"alpha-(1,3)-fucosyltransferase 4",FUT4,HGNC:4015,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD16,,Ideal exclusion|Required exclusion|Required phenotypic markers,PR:000001483,low affinity immunoglobulin gamma Fc region receptor III,,low affinity immunoglobulin gamma Fc region receptor III,,,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD161,,Ideal phenotypic markers|Required phenotypic markers,PR:Q12918,killer cell lectin-like receptor subfamily B member 1 (human),Q12918,killer cell lectin-like receptor subfamily B member 1 (human),KLRB1,HGNC:6373,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD172a,,Ideal phenotypic markers,PR:000001968,tyrosine-protein phosphatase non-receptor type substrate 1,P78324,tyrosine-protein phosphatase non-receptor type substrate 1,SIRPA,HGNC:9662,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD183,CXCR3|CD183,Required phenotypic markers,PR:000001207,C-X-C chemokine receptor type 3,P49682,C-X-C chemokine receptor type 3,CXCR3,HGNC:4540,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD185,CXCR5|CD185,Required phenotypic markers,PR:000001209,C-X-C chemokine receptor type 5,P32302,C-X-C chemokine receptor type 5,CXCR5,HGNC:1060,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD19,,Ideal exclusion|Required exclusion|Required phenotypic markers,PR:000001002,CD19 molecule,P15391,CD19 molecule,CD19,HGNC:1633,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD193,,Required exclusion|Required phenotypic markers,PR:000001255,C-C chemokine receptor type 3,P51677,C-C chemokine receptor type 3,CCR3,HGNC:1604,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD194,CCR4|CD194,Required phenotypic markers,PR:000001200,C-C chemokine receptor type 4,P51679,C-C chemokine receptor type 4,CCR4,HGNC:1605,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD196,CCR6|CD196,Required phenotypic markers,PR:000001202,C-C chemokine receptor type 6,P51684,C-C chemokine receptor type 6,CCR6,HGNC:1607,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD198,,Ideal phenotypic markers,PR:000001204,C-C chemokine receptor type 8,,C-C chemokine receptor type 8,,,,ols4,high,https://www.ebi.ac.uk/ols4/api/search?q=CCR8&ontology=pr; https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=PR:000001204, +CD1c,,Required phenotypic markers,PR:000002027,T-cell surface glycoprotein CD1c,P29017,T-cell surface glycoprotein CD1c,CD1C,HGNC:1636,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD1d-a-GalCer,,Required phenotypic markers,,,,,,,,manual,low,,lipid antigen (alpha-galactosylceramide) presented by CD1d; not a protein marker +CD20,,Ideal phenotypic markers|Required exclusion|Required phenotypic markers,PR:000001289,membrane-spanning 4-domains subfamily A member 1,P11836,membrane-spanning 4-domains subfamily A member 1,MS4A1,HGNC:7315,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD21,,Required phenotypic markers,PR:000001338,complement receptor type 2,P20023,complement receptor type 2,CR2,HGNC:2336,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD24,,Required phenotypic markers,PR:000001932,signal transducer CD24,P25063,signal transducer CD24,CD24,HGNC:1645,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD25,,Required phenotypic markers,PR:000001380,interleukin-2 receptor subunit alpha,P01589,interleukin-2 receptor subunit alpha,IL2RA,HGNC:6008,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD27,,Required phenotypic markers,PR:000001963,CD27 molecule,P26842,CD27 molecule,CD27,HGNC:11922,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD294,,Ideal phenotypic markers|Required phenotypic markers,PR:Q9Y5Y4,prostaglandin D2 receptor 2 (human),Q9Y5Y4,prostaglandin D2 receptor 2 (human),PTGDR2,HGNC:4502,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD3,,Ideal exclusion|Required exclusion|Required phenotypic markers,PR:000001020,CD3 epsilon,P07766,CD3 epsilon,CD3E,HGNC:1674,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD303,,Required exclusion|Required phenotypic markers,PR:000001292,C-type lectin domain family 4 member C,Q8WTT0,C-type lectin domain family 4 member C,CLEC4C,HGNC:13258,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD33,,Ideal phenotypic markers|Required exclusion|Required phenotypic markers,PR:000001892,CD33 molecule,P20138,CD33 molecule,CD33,HGNC:1659,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD34,,Required exclusion,PR:000001003,CD34 molecule,P28906,CD34 molecule,CD34,HGNC:1662,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD38,,Required phenotypic markers,PR:000001408,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,P28907,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,CD38,HGNC:1667,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD4,,Required phenotypic markers,PR:000001004,CD4 molecule,P01730,CD4 molecule,CD4,HGNC:1678,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD45,,Required phenotypic markers,PR:000001006,receptor-type tyrosine-protein phosphatase C,P08575,receptor-type tyrosine-protein phosphatase C,PTPRC,HGNC:9666,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD56,,Ideal exclusion|Required exclusion|Required phenotypic markers,PR:000001024,neural cell adhesion molecule 1,P13591,neural cell adhesion molecule 1,NCAM1,HGNC:7656,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD57,,Required phenotypic markers,,,,,,,,ols4,low,https://www.ebi.ac.uk/ols4/api/search?q=CD57&ontology=pr,B3GAT1 / HNK-1 epitope; HNK-1 carbohydrate epitope synthesised by B3GAT1 +CD64,,Ideal phenotypic markers|Required exclusion|Required phenotypic markers,PR:000001465,high affinity immunoglobulin gamma Fc receptor I,P12314,high affinity immunoglobulin gamma Fc receptor I,FCGR1A,HGNC:3613,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD66b,,Ideal exclusion|Required exclusion|Required phenotypic markers,PR:000001332,cell adhesion molecule CEACAM8,P31997,cell adhesion molecule CEACAM8,CEACAM8,HGNC:1820,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CD8,,Required phenotypic markers,PR:000001084,T-cell surface glycoprotein CD8 alpha chain,P01732,T-cell surface glycoprotein CD8 alpha chain,CD8A,HGNC:1706,,cl_pro_tsv,high,reports/cl_pro_relationships.tsv, +CXCR3,CXCR3|CD183,Required phenotypic markers,PR:000001207,C-X-C chemokine receptor type 3,P49682,C-X-C chemokine receptor type 3,CXCR3,HGNC:4540,,inferred,high,reports/cl_pro_relationships.tsv, +CXCR5,CXCR5|CD185,Required phenotypic markers,PR:000001209,C-X-C chemokine receptor type 5,P32302,C-X-C chemokine receptor type 5,CXCR5,HGNC:1060,,inferred,high,reports/cl_pro_relationships.tsv, +FceR1a,,Ideal phenotypic markers|Required phenotypic markers,PR:000007431,high affinity immunoglobulin epsilon receptor subunit alpha,,high affinity immunoglobulin epsilon receptor subunit alpha,,,,ols4,high,https://www.ebi.ac.uk/ols4/api/search?q=FCER1A&ontology=pr; https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=PR:000007431,high-affinity IgE receptor alpha chain +HLA-DR,,Ideal exclusion|Ideal phenotypic markers|Required phenotypic markers,PR:000002015,MHC class II histocompatibility antigen alpha chain DRA,,MHC class II histocompatibility antigen alpha chain DRA,,,,ols4,high,https://www.ebi.ac.uk/ols4/api/search?q=HLA-DRA&ontology=pr; https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=PR:000002015,HLA-DR is a heterodimer of HLA-DRA + HLA-DRB1; mapped to HLA-DRA as primary chain +IFNg,,Ideal phenotypic markers,,,P01579,interferon gamma,IFNG,HGNC:5438,,monarch,high,https://rest.genenames.org/fetch/symbol/IFNG,intracellular marker +IL-13,,Ideal phenotypic markers,,,P35225,interleukin 13,IL13,HGNC:5973,,monarch,high,https://rest.genenames.org/fetch/symbol/IL13,intracellular marker +IL-17a,,Ideal phenotypic markers,,,Q16552,interleukin 17A,IL17A,HGNC:5981,,monarch,high,https://rest.genenames.org/fetch/symbol/IL17A,intracellular marker +IL-4,,Ideal phenotypic markers,,,P05112,interleukin 4,IL4,HGNC:6014,,monarch,high,https://rest.genenames.org/fetch/symbol/IL4,intracellular marker +IL-5,,Ideal phenotypic markers,,,P05113,interleukin 5,IL5,HGNC:6016,,monarch,high,https://rest.genenames.org/fetch/symbol/IL5,intracellular marker +IL-9,,Ideal phenotypic markers,,,P15248,interleukin 9,IL9,HGNC:6029,,monarch,high,https://rest.genenames.org/fetch/symbol/IL9,intracellular marker +IgA,,Required phenotypic markers,,,,,,,,manual,low,,Immunoglobulin heavy-chain class A; encoded by IGHA1 and IGHA2 gene family. No single PR ID or UniProt accession covers all isotypes. +IgD,,Required phenotypic markers,,,,,,,,manual,low,,Immunoglobulin heavy-chain class D; encoded by IGHD. No single PR ID or UniProt accession. +IgE,,Required phenotypic markers,,,,,,,,manual,low,,Immunoglobulin heavy-chain class E; encoded by IGHE. No single PR ID or UniProt accession. +IgG,,Required phenotypic markers,,,,,,,,manual,low,,Immunoglobulin heavy-chain class G; encoded by IGHG1/IGHG2/IGHG3/IGHG4 gene family. No single PR ID or UniProt accession covers all subclasses. +IgM,,Required phenotypic markers,,,,,,,,manual,low,,Immunoglobulin heavy-chain class M; encoded by IGHM. No single PR ID or UniProt accession. +MR1,,Required phenotypic markers,,,Q95460,"major histocompatibility complex, class I-related",MR1,HGNC:4975,,manual,high,https://rest.genenames.org/fetch/symbol/MR1,MHC-related protein 1; also used as 'MR1 tetramer' reagent for MAIT cell detection +TCR,,Ideal phenotypic markers|Required phenotypic markers,,,,,,,,manual,medium,,pan-TCR marker; not specific to a single gene +TCRVa24,,Required phenotypic markers,,,,,TRAV10,HGNC:12103,,manual,medium,https://rest.genenames.org/fetch/symbol/TRAV10,IMGT nomenclature: TRAV10 +TCRVa24-Ja18,,Required phenotypic markers,,,,,TRAV10,HGNC:12103,,manual,medium,https://rest.genenames.org/fetch/symbol/TRAV10,Invariant iNKT TCR chain; two-gene marker TRAV10+TRAJ18; gene_symbol populated with TRAV10 as primary TRAV gene +TCRVa7.2,,Required phenotypic markers,,,,,TRAV1-2,HGNC:12102,,manual,medium,https://rest.genenames.org/fetch/symbol/TRAV1-2,IMGT nomenclature: TRAV1-2 +TCRVb11,,Required phenotypic markers,,,,,TRBV25-1,HGNC:12205,,manual,medium,https://rest.genenames.org/fetch/symbol/TRBV25-1,IMGT nomenclature: TRBV25-1 +TCRVd2,,Required phenotypic markers,,,,,TRDV2,HGNC:12263,,manual,medium,https://rest.genenames.org/fetch/symbol/TRDV2,IMGT nomenclature: TRDV2 +TCRVg9,,Required phenotypic markers,,,,,TRGV9,HGNC:12295,,manual,medium,https://rest.genenames.org/fetch/symbol/TRGV9,IMGT nomenclature: TRGV9 +TCRab,,Required phenotypic markers,,,,,,,,manual,medium,,pan-αβ TCR marker; recognises assembled αβ heterodimer +TCRgd,,Required phenotypic markers,,,,,,,,manual,medium,,pan-γδ TCR marker; recognises assembled γδ heterodimer +TCRva24,,Required phenotypic markers,,,,,TRAV10,HGNC:12103,,manual,medium,https://rest.genenames.org/fetch/symbol/TRAV10,Likely duplicate of TCRVa24 (different capitalisation) — data quality issue; mapped identically to TCRVa24 / TRAV10 +Tetramer,,Required phenotypic markers,,,,,,,,manual,low,,generic reagent term; not a specific protein +V,,Ideal phenotypic markers|Required phenotypic markers,,,,,,,,manual,low,,likely parsing artifact from multi-word TCR gene name — data quality issue; see reports/marker_validation.md +VB11,,Required phenotypic markers,,,,,TRBV25-1,HGNC:12205,,manual,medium,https://rest.genenames.org/fetch/symbol/TRBV25-1,Duplicate of TCRVb11 (uppercase) — data quality issue; same mapping as TCRVb11 / TRBV25-1 +Vb11,,Required phenotypic markers,,,,,TRBV25-1,HGNC:12205,,manual,medium,https://rest.genenames.org/fetch/symbol/TRBV25-1,Duplicate of TCRVb11 — data quality issue; same mapping as TCRVb11 / TRBV25-1 +Vd1,,Required phenotypic markers,,,,,TRDV1,HGNC:12262,,manual,medium,https://rest.genenames.org/fetch/symbol/TRDV1,IMGT nomenclature: TRDV1 +delta,,Ideal phenotypic markers|Required phenotypic markers,,,,,,,,manual,low,,likely parsing artifact from multi-word TCR gene name — data quality issue; see reports/marker_validation.md +delta1,,Ideal phenotypic markers,,,,,,,,manual,low,,likely parsing artifact from multi-word TCR gene name — data quality issue; see reports/marker_validation.md +gamma,,Ideal phenotypic markers|Required phenotypic markers,,,,,,,,manual,low,,likely parsing artifact from multi-word TCR gene name — data quality issue; see reports/marker_validation.md diff --git a/marker_mappings/marker_tokens.csv b/marker_mappings/marker_tokens.csv new file mode 100644 index 0000000..5d8037e --- /dev/null +++ b/marker_mappings/marker_tokens.csv @@ -0,0 +1,76 @@ +marker_token,source_columns,cell_types +CCR4,Required phenotypic markers, +CCR6,Required phenotypic markers, +CD10,Required phenotypic markers, +CD117,Required phenotypic markers, +CD11c,Ideal exclusion|Required phenotypic markers, +CD123,Ideal exclusion|Required exclusion|Required phenotypic markers, +CD127,Ideal exclusion|Required phenotypic markers, +CD138,Required phenotypic markers, +CD14,Ideal exclusion|Required exclusion|Required phenotypic markers, +CD141,Required phenotypic markers, +CD15,Ideal exclusion|Required exclusion|Required phenotypic markers, +CD16,Ideal exclusion|Required exclusion|Required phenotypic markers, +CD161,Ideal phenotypic markers|Required phenotypic markers, +CD172a,Ideal phenotypic markers, +CD183,Required phenotypic markers, +CD185,Required phenotypic markers, +CD19,Ideal exclusion|Required exclusion|Required phenotypic markers, +CD193,Required exclusion|Required phenotypic markers, +CD194,Required phenotypic markers, +CD196,Required phenotypic markers, +CD198,Ideal phenotypic markers, +CD1c,Required phenotypic markers, +CD1d-a-GalCer,Required phenotypic markers, +CD20,Ideal phenotypic markers|Required exclusion|Required phenotypic markers, +CD21,Required phenotypic markers, +CD24,Required phenotypic markers, +CD25,Required phenotypic markers, +CD27,Required phenotypic markers, +CD294,Ideal phenotypic markers|Required phenotypic markers, +CD3,Ideal exclusion|Required exclusion|Required phenotypic markers, +CD303,Required exclusion|Required phenotypic markers, +CD33,Ideal phenotypic markers|Required exclusion|Required phenotypic markers, +CD34,Required exclusion, +CD38,Required phenotypic markers, +CD4,Required phenotypic markers, +CD45,Required phenotypic markers, +CD56,Ideal exclusion|Required exclusion|Required phenotypic markers, +CD57,Required phenotypic markers, +CD64,Ideal phenotypic markers|Required exclusion|Required phenotypic markers, +CD66b,Ideal exclusion|Required exclusion|Required phenotypic markers, +CD8,Required phenotypic markers, +CXCR3,Required phenotypic markers, +CXCR5,Required phenotypic markers, +FceR1a,Ideal phenotypic markers|Required phenotypic markers, +HLA-DR,Ideal exclusion|Ideal phenotypic markers|Required phenotypic markers, +IFNg,Ideal phenotypic markers, +IL-13,Ideal phenotypic markers, +IL-17a,Ideal phenotypic markers, +IL-4,Ideal phenotypic markers, +IL-5,Ideal phenotypic markers, +IL-9,Ideal phenotypic markers, +IgA,Required phenotypic markers, +IgD,Required phenotypic markers, +IgE,Required phenotypic markers, +IgG,Required phenotypic markers, +IgM,Required phenotypic markers, +MR1,Required phenotypic markers, +TCR,Ideal phenotypic markers|Required phenotypic markers, +TCRVa24,Required phenotypic markers, +TCRVa24-Ja18,Required phenotypic markers, +TCRVa7.2,Required phenotypic markers, +TCRVb11,Required phenotypic markers, +TCRVd2,Required phenotypic markers, +TCRVg9,Required phenotypic markers, +TCRab,Required phenotypic markers, +TCRgd,Required phenotypic markers, +TCRva24,Required phenotypic markers, +Tetramer,Required phenotypic markers, +V,Ideal phenotypic markers|Required phenotypic markers, +VB11,Required phenotypic markers, +Vb11,Required phenotypic markers, +Vd1,Required phenotypic markers, +delta,Ideal phenotypic markers|Required phenotypic markers, +delta1,Ideal phenotypic markers, +gamma,Ideal phenotypic markers|Required phenotypic markers, diff --git a/pyproject.toml b/pyproject.toml index e60a335..14e18cc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,6 +23,7 @@ soulcap-lookup = "soulcap_cl_mapping.ols4_lookup:main" soulcap-match = "soulcap_cl_mapping.cl_match:main" soulcap-tokens = "soulcap_cl_mapping.marker_syntax:tokens_main" soulcap-hgnc = "soulcap_cl_mapping.hgnc_map:main" +soulcap-map = "soulcap_cl_mapping.marker_map:main" [project.optional-dependencies] dev = [ diff --git a/src/soulcap_cl_mapping/marker_map.py b/src/soulcap_cl_mapping/marker_map.py new file mode 100644 index 0000000..2117869 --- /dev/null +++ b/src/soulcap_cl_mapping/marker_map.py @@ -0,0 +1,968 @@ +"""Build ``marker_mappings/marker_protein_gene.csv`` — Milestone 1 deliverable. + +Maps every SOULCAP marker token (from ``marker_mappings/marker_tokens.csv``) to its +protein and gene identifiers, using three primary sources: + +* ``reports/cl_pro_relationships.tsv`` — CL→PR axiom snapshot (Groups 1 & 2) +* EBI OLS4 REST API — PR ontology term lookup (Group 3) +* Monarch Node Normalizer — UniProt → HGNC resolution (Groups 3 & 4) +* HGNC REST API — gene symbol → HGNC ID (Groups 4, 6, 7) + +Usage:: + + soulcap-map # generate marker_mappings/marker_protein_gene.csv + soulcap-map --dry-run # print summary without writing + soulcap-map --out path.csv # write to an alternative path +""" + +from __future__ import annotations + +import argparse +import csv +import sys +import time +from pathlib import Path +from typing import Any + +import requests + +from soulcap_cl_mapping.hgnc_map import fetch_normalized_nodes + +REPO_ROOT = Path(__file__).resolve().parents[2] +MARKER_TOKENS_CSV = REPO_ROOT / "marker_mappings" / "marker_tokens.csv" +CL_PRO_TSV = REPO_ROOT / "reports" / "cl_pro_relationships.tsv" +OUTPUT_CSV = REPO_ROOT / "marker_mappings" / "marker_protein_gene.csv" + +MONARCH_URL = "https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes" +HGNC_REST_URL = "https://rest.genenames.org" +OLS4_BASE = "https://www.ebi.ac.uk/ols4/api" + +OUTPUT_FIELDS = [ + "marker_token", + "marker_synonyms", + "source_columns", + "pro_id", + "pro_label", + "uniprot_id", + "uniprot_label", + "gene_symbol", + "hgnc_id", + "ncbi_gene_id", + "mapping_method", + "confidence", + "evidence", + "notes", +] + +# --------------------------------------------------------------------------- # +# Static configuration for non-API groups +# --------------------------------------------------------------------------- # + +# Group 2: common-name aliases that resolve to an already-mapped Group 1 token. +# key = alias token, value = canonical CD token (Group 1) +ALIAS_MAP: dict[str, str] = { + "CCR4": "CD194", + "CCR6": "CD196", + "CXCR3": "CD183", + "CXCR5": "CD185", +} + +# Group 3: tokens that require an OLS4 PR search. +# key = marker token, value = dict with 'query' (OLS4 search string) and 'notes'. +GROUP3_CONFIG: dict[str, dict[str, str]] = { + "CD57": { + "query": "CD57", + "notes": "B3GAT1 / HNK-1 epitope; HNK-1 carbohydrate epitope synthesised by B3GAT1", + }, + "CD198": { + "query": "CCR8", + "notes": "", + }, + "FceR1a": { + "query": "FCER1A", + "notes": "high-affinity IgE receptor alpha chain", + }, + "HLA-DR": { + "query": "HLA-DRA", + "notes": ( + "HLA-DR is a heterodimer of HLA-DRA + HLA-DRB1; " + "mapped to HLA-DRA as primary chain" + ), + }, +} + +# Group 4: cytokine / intracellular staining markers. +# key = marker token, value = approved HGNC gene symbol +GROUP4_GENE_SYMBOLS: dict[str, str] = { + "IFNg": "IFNG", + "IL-4": "IL4", + "IL-5": "IL5", + "IL-9": "IL9", + "IL-13": "IL13", + "IL-17a": "IL17A", +} + +# Group 5: immunoglobulin class markers (multi-gene, manual). +# key = marker token, value = notes string +GROUP5_NOTES: dict[str, str] = { + "IgA": ( + "Immunoglobulin heavy-chain class A; encoded by IGHA1 and IGHA2 gene family. " + "No single PR ID or UniProt accession covers all isotypes." + ), + "IgD": ( + "Immunoglobulin heavy-chain class D; encoded by IGHD. " + "No single PR ID or UniProt accession." + ), + "IgE": ( + "Immunoglobulin heavy-chain class E; encoded by IGHE. " + "No single PR ID or UniProt accession." + ), + "IgG": ( + "Immunoglobulin heavy-chain class G; encoded by IGHG1/IGHG2/IGHG3/IGHG4 gene " + "family. No single PR ID or UniProt accession covers all subclasses." + ), + "IgM": ( + "Immunoglobulin heavy-chain class M; encoded by IGHM. " + "No single PR ID or UniProt accession." + ), +} + +# Group 6: TCR variable gene segment markers. +# Tokens with a 1:1 gene mapping (these need an HGNC lookup). +TCR_GENE_TOKENS: dict[str, str] = { + "TCRVa24": "TRAV10", + "TCRVa7.2": "TRAV1-2", + "TCRVb11": "TRBV25-1", + "TCRVd2": "TRDV2", + "TCRVg9": "TRGV9", + "Vd1": "TRDV1", +} + +# Group 6: tokens with specific notes but no direct gene or needing special handling. +TCR_SPECIAL_NOTES: dict[str, str] = { + "TCR": "pan-TCR marker; not specific to a single gene", + "TCRab": "pan-αβ TCR marker; recognises assembled αβ heterodimer", + "TCRgd": "pan-γδ TCR marker; recognises assembled γδ heterodimer", + "TCRVa24-Ja18": ( + "Invariant iNKT TCR chain; two-gene marker TRAV10+TRAJ18; " + "gene_symbol populated with TRAV10 as primary TRAV gene" + ), + "TCRva24": ( + "Likely duplicate of TCRVa24 (different capitalisation) — data quality issue; " + "mapped identically to TCRVa24 / TRAV10" + ), + "Vb11": "Duplicate of TCRVb11 — data quality issue; same mapping as TCRVb11 / TRBV25-1", + "VB11": "Duplicate of TCRVb11 (uppercase) — data quality issue; same mapping as TCRVb11 / TRBV25-1", +} + +# Duplication map: tokens that are duplicates of gene-resolved tokens in Group 6. +TCR_DUPLICATE_OF: dict[str, str] = { + "TCRva24": "TCRVa24", + "Vb11": "TCRVb11", + "VB11": "TCRVb11", + "TCRVa24-Ja18": "TCRVa24", # same TRAV10 gene, special note +} + +# Group 7: non-protein / complex markers. +GROUP7_NOTES: dict[str, str] = { + "Tetramer": "generic reagent term; not a specific protein", + "CD1d-a-GalCer": ( + "lipid antigen (alpha-galactosylceramide) presented by CD1d; " + "not a protein marker" + ), + "MR1": ( + "MHC-related protein 1; also used as 'MR1 tetramer' reagent for MAIT cell detection" + ), +} + +# Group 8: parsing artifacts. +ARTIFACT_TOKENS: frozenset[str] = frozenset({"V", "delta", "delta1", "gamma"}) + + +# --------------------------------------------------------------------------- # +# File I/O +# --------------------------------------------------------------------------- # + + +def load_marker_tokens(path: Path) -> list[dict[str, str]]: + """Load ``marker_tokens.csv`` into a list of row dicts.""" + with open(path, encoding="utf-8", newline="") as fh: + reader = csv.DictReader(fh) + return [dict(row) for row in reader] + + +def load_tsv_rows(path: Path) -> list[dict[str, str]]: + """Load a TSV file into a list of row dicts.""" + with open(path, encoding="utf-8", newline="") as fh: + reader = csv.DictReader(fh, delimiter="\t") + return [dict(row) for row in reader] + + +def write_csv(path: Path, rows: list[dict[str, str]]) -> None: + """Write the output CSV with a fixed field order.""" + with open(path, "w", encoding="utf-8", newline="") as fh: + writer = csv.DictWriter( + fh, + fieldnames=OUTPUT_FIELDS, + extrasaction="ignore", + lineterminator="\n", + ) + writer.writeheader() + writer.writerows(rows) + + +# --------------------------------------------------------------------------- # +# TSV synonym lookup (Group 1) +# --------------------------------------------------------------------------- # + + +def parse_cd_synonyms(cd_synonym_str: str) -> list[tuple[str, str]]: + """Parse ``cd_synonym`` cell text into (name, qualifier) pairs. + + Example input: ``"CD19 (label); CD19A (exact)"`` + Returns: ``[("CD19", "label"), ("CD19A", "exact")]`` + """ + if not cd_synonym_str: + return [] + results: list[tuple[str, str]] = [] + for part in cd_synonym_str.split(";"): + part = part.strip() + if "(" in part and ")" in part: + close = part.rfind(")") + open_ = part.rfind("(", 0, close) + name = part[:open_].strip() + qualifier = part[open_ + 1 : close].strip() + else: + name = part + qualifier = "" + if name: + results.append((name, qualifier)) + return results + + +def _row_score(row: dict[str, str], qualifier: str) -> int: + """Score a (row, qualifier) candidate for synonym lookup preference. + + Priority (highest wins): + * +2 if the synonym qualifier is "label" (canonical PR name) + * +1 if the row has a non-empty ``hgnc_id`` (canonical species-independent PR) + + Rows with both score 3 (best); isoform-specific rows typically lack ``hgnc_id`` + and score lower than their canonical counterparts. + """ + score = 0 + if qualifier.lower() == "label": + score += 2 + if row.get("hgnc_id"): + score += 1 + return score + + +def build_synonym_lookup(rows: list[dict[str, str]]) -> dict[str, dict[str, str]]: + """Build an uppercase-token -> best PR row mapping from TSV rows. + + When multiple rows share the same uppercase CD synonym, the function selects + the one with the highest :func:`_row_score` (label + HGNC > label > HGNC > + first occurrence), ensuring canonical entries win over isoform-specific ones. + """ + # Map uppercase synonym → list of (row, qualifier) + raw: dict[str, list[tuple[dict[str, str], str]]] = {} + for row in rows: + for name, qualifier in parse_cd_synonyms(row.get("cd_synonym", "")): + key = name.upper() + raw.setdefault(key, []).append((row, qualifier)) + + lookup: dict[str, dict[str, str]] = {} + for key, candidates in raw.items(): + best_row: dict[str, str] | None = None + best_score = -1 + for row, qualifier in candidates: + score = _row_score(row, qualifier) + if score > best_score: + best_score = score + best_row = row + if best_row is not None: + lookup[key] = best_row + return lookup + + +def _strip_uniprot_prefix(value: str) -> str: + """Return first UniProtKB accession from a possibly-multi-valued field.""" + if not value: + return "" + first = value.split(";")[0].strip() + return first.replace("UniProtKB:", "") + + +# --------------------------------------------------------------------------- # +# Network helpers for Groups 3, 4, 6, 7 +# --------------------------------------------------------------------------- # + + +def search_ols4_pr( + query: str, + session: requests.Session, + ols4_url: str = OLS4_BASE, +) -> dict[str, str] | None: + """Search OLS4 PR ontology for *query*. + + Returns a dict with ``pr_id`` and ``pr_label``, or ``None`` if nothing found. + """ + params: dict[str, Any] = { + "q": query, + "ontology": "pr", + "rows": 5, + "exact": "false", + } + resp = session.get(f"{ols4_url}/search", params=params, timeout=30) + resp.raise_for_status() + docs = resp.json().get("response", {}).get("docs", []) + for doc in docs: + obo_id = doc.get("obo_id", "") + if obo_id.startswith("PR:"): + return {"pr_id": obo_id, "pr_label": doc.get("label", "")} + return None + + +def fetch_hgnc_by_symbol( + symbol: str, + session: requests.Session, + hgnc_url: str = HGNC_REST_URL, +) -> dict[str, str] | None: + """Fetch an HGNC gene record by approved gene symbol. + + Returns a dict with ``hgnc_id``, ``gene_symbol``, ``uniprot_id``, and ``name``; + or ``None`` if the symbol is not found. + + The HGNC REST API response:: + + {"response": {"numFound": 1, "docs": [{ + "hgnc_id": "HGNC:5438", + "symbol": "IFNG", + "name": "interferon gamma", + "uniprot_ids": ["P01579"], + ... + }]}} + """ + url = f"{hgnc_url}/fetch/symbol/{symbol}" + resp = session.get(url, timeout=30, headers={"Accept": "application/json"}) + resp.raise_for_status() + docs = resp.json().get("response", {}).get("docs", []) + if not docs: + return None + doc = docs[0] + raw_hgnc = doc.get("hgnc_id", "") + hgnc_id = raw_hgnc if raw_hgnc.startswith("HGNC:") else f"HGNC:{raw_hgnc}" + uniprot_ids: list[str] = doc.get("uniprot_ids", []) or [] + return { + "hgnc_id": hgnc_id, + "gene_symbol": doc.get("symbol", symbol), + "uniprot_id": uniprot_ids[0] if uniprot_ids else "", + "name": doc.get("name", ""), + } + + +def extract_monarch_identifiers(node: dict[str, Any]) -> dict[str, str]: + """Extract HGNC ID, gene symbol, UniProt accession, and NCBI Gene ID. + + Canonical UniProt accessions (no isoform suffix '-N') are preferred. + """ + result: dict[str, str] = { + "hgnc_id": "", + "gene_symbol": "", + "uniprot_id": "", + "ncbi_gene_id": "", + } + for entry in node.get("equivalent_identifiers", []): + ident = entry.get("identifier", "") + label = entry.get("label", "") + if ident.startswith("HGNC:") and not result["hgnc_id"]: + result["hgnc_id"] = ident + result["gene_symbol"] = label + elif ( + ident.startswith("UniProtKB:") + and not result["uniprot_id"] + and "-" not in ident + ): + result["uniprot_id"] = ident.replace("UniProtKB:", "") + elif ident.startswith("NCBIGene:") and not result["ncbi_gene_id"]: + result["ncbi_gene_id"] = ident.replace("NCBIGene:", "") + return result + + +# --------------------------------------------------------------------------- # +# Group resolvers +# --------------------------------------------------------------------------- # + + +def _empty_row( + token: str, + source_columns: str, + method: str, + confidence: str, + notes: str = "", + evidence: str = "", +) -> dict[str, str]: + """Return a row with all protein/gene fields empty.""" + return { + "marker_token": token, + "marker_synonyms": "", + "source_columns": source_columns, + "pro_id": "", + "pro_label": "", + "uniprot_id": "", + "uniprot_label": "", + "gene_symbol": "", + "hgnc_id": "", + "ncbi_gene_id": "", + "mapping_method": method, + "confidence": confidence, + "evidence": evidence, + "notes": notes, + } + + +def resolve_group1( + token: str, + source_columns: str, + synonym_lookup: dict[str, dict[str, str]], + alias_reverse: dict[str, str], +) -> dict[str, str] | None: + """Resolve a Group 1 token from the CL-PRO TSV synonym lookup. + + *alias_reverse* maps canonical CD names to their alias tokens (e.g. CD183 → CXCR3), + used to populate ``marker_synonyms``. + + Returns ``None`` if the token has no CD synonym match. + """ + key = token.upper() + row = synonym_lookup.get(key) + if row is None: + return None + + uniprot_id = _strip_uniprot_prefix(row.get("uniprot_human", "")) + pr_id = row.get("pr", "") + + # Populate cross-synonyms: if this token has an alias (e.g. CD183 ↔ CXCR3) + alias = alias_reverse.get(token, "") + synonyms = f"{alias}|{token}" if alias else "" + + return { + "marker_token": token, + "marker_synonyms": synonyms, + "source_columns": source_columns, + "pro_id": pr_id, + "pro_label": row.get("pr_label", ""), + "uniprot_id": uniprot_id, + "uniprot_label": row.get("pr_label", ""), # PR label as proxy for protein name + "gene_symbol": row.get("hgnc_symbol", ""), + "hgnc_id": row.get("hgnc_id", ""), + "ncbi_gene_id": "", + "mapping_method": "cl_pro_tsv", + "confidence": "high", + "evidence": "reports/cl_pro_relationships.tsv", + "notes": "", + } + + +def resolve_group2( + token: str, + source_columns: str, + canonical_token: str, + resolved_g1: dict[str, dict[str, str]], +) -> dict[str, str]: + """Resolve a Group 2 alias token by copying Group 1 data.""" + canonical = resolved_g1.get(canonical_token) + if canonical is None: + return _empty_row( + token, + source_columns, + method="inferred", + confidence="high", + notes=f"alias for {canonical_token}; canonical entry not yet resolved", + ) + row = dict(canonical) + row["marker_token"] = token + row["source_columns"] = source_columns + row["mapping_method"] = "inferred" + # Synonyms: both names separated by | + row["marker_synonyms"] = f"{token}|{canonical_token}" + return row + + +def resolve_group3( + token: str, + source_columns: str, + config: dict[str, str], + session: requests.Session, + ols4_url: str = OLS4_BASE, + monarch_url: str = MONARCH_URL, + sleep_between: float = 0.2, +) -> dict[str, str]: + """Resolve a Group 3 token via OLS4 PR search then Monarch HGNC lookup.""" + query = config.get("query", token) + notes = config.get("notes", "") + + pr_result = search_ols4_pr(query, session, ols4_url=ols4_url) + pr_id = pr_result["pr_id"] if pr_result else "" + pr_label = pr_result["pr_label"] if pr_result else "" + + # Monarch lookup for HGNC + UniProt + hgnc_id = gene_symbol = uniprot_id = ncbi_gene_id = "" + evidence = f"{ols4_url}/search?q={query}&ontology=pr" + if pr_id: + if sleep_between > 0: + time.sleep(sleep_between) + nodes = fetch_normalized_nodes([pr_id], session=session, url=monarch_url) + node = nodes.get(pr_id, {}) + if node: + ids = extract_monarch_identifiers(node) + hgnc_id = ids["hgnc_id"] + gene_symbol = ids["gene_symbol"] + uniprot_id = ids["uniprot_id"] + ncbi_gene_id = ids["ncbi_gene_id"] + evidence += f"; {monarch_url}?curie={pr_id}" + + return { + "marker_token": token, + "marker_synonyms": "", + "source_columns": source_columns, + "pro_id": pr_id, + "pro_label": pr_label, + "uniprot_id": uniprot_id, + "uniprot_label": pr_label, + "gene_symbol": gene_symbol, + "hgnc_id": hgnc_id, + "ncbi_gene_id": ncbi_gene_id, + "mapping_method": "ols4", + "confidence": "high" if pr_id else "low", + "evidence": evidence, + "notes": notes, + } + + +def resolve_group4( + token: str, + source_columns: str, + gene_symbol: str, + session: requests.Session, + hgnc_url: str = HGNC_REST_URL, + sleep_between: float = 0.2, +) -> dict[str, str]: + """Resolve a Group 4 cytokine token via the HGNC REST API.""" + hgnc_data = fetch_hgnc_by_symbol(gene_symbol, session, hgnc_url=hgnc_url) + + if sleep_between > 0: + time.sleep(sleep_between) + + hgnc_id = hgnc_data["hgnc_id"] if hgnc_data else "" + approved_symbol = hgnc_data["gene_symbol"] if hgnc_data else gene_symbol + uniprot_id = hgnc_data["uniprot_id"] if hgnc_data else "" + protein_name = hgnc_data["name"] if hgnc_data else "" + evidence = f"{hgnc_url}/fetch/symbol/{gene_symbol}" + + return { + "marker_token": token, + "marker_synonyms": "", + "source_columns": source_columns, + "pro_id": "", + "pro_label": "", + "uniprot_id": uniprot_id, + "uniprot_label": protein_name, + "gene_symbol": approved_symbol, + "hgnc_id": hgnc_id, + "ncbi_gene_id": "", + "mapping_method": "monarch", + "confidence": "high" if hgnc_id else "low", + "evidence": evidence, + "notes": "intracellular marker", + } + + +def resolve_group6_gene_token( + token: str, + source_columns: str, + imgt_gene: str, + extra_notes: str, + session: requests.Session, + hgnc_url: str = HGNC_REST_URL, + sleep_between: float = 0.2, +) -> dict[str, str]: + """Resolve a Group 6 TCR gene token via the HGNC REST API.""" + hgnc_data = fetch_hgnc_by_symbol(imgt_gene, session, hgnc_url=hgnc_url) + + if sleep_between > 0: + time.sleep(sleep_between) + + hgnc_id = hgnc_data["hgnc_id"] if hgnc_data else "" + approved_symbol = hgnc_data["gene_symbol"] if hgnc_data else imgt_gene + evidence = f"{hgnc_url}/fetch/symbol/{imgt_gene}" + + base_note = f"IMGT nomenclature: {imgt_gene}" + notes = f"{base_note}; {extra_notes}" if extra_notes else base_note + + return { + "marker_token": token, + "marker_synonyms": "", + "source_columns": source_columns, + "pro_id": "", + "pro_label": "", + "uniprot_id": "", + "uniprot_label": "", + "gene_symbol": approved_symbol, + "hgnc_id": hgnc_id, + "ncbi_gene_id": "", + "mapping_method": "manual", + "confidence": "medium", + "evidence": evidence, + "notes": notes, + } + + +def resolve_group7_mr1( + token: str, + source_columns: str, + session: requests.Session, + hgnc_url: str = HGNC_REST_URL, + sleep_between: float = 0.2, +) -> dict[str, str]: + """Resolve MR1 (MHC-related protein 1) via the HGNC REST API.""" + hgnc_data = fetch_hgnc_by_symbol("MR1", session, hgnc_url=hgnc_url) + + if sleep_between > 0: + time.sleep(sleep_between) + + hgnc_id = hgnc_data["hgnc_id"] if hgnc_data else "" + approved_symbol = hgnc_data["gene_symbol"] if hgnc_data else "MR1" + uniprot_id = hgnc_data["uniprot_id"] if hgnc_data else "" + protein_name = hgnc_data["name"] if hgnc_data else "" + evidence = f"{hgnc_url}/fetch/symbol/MR1" + + return { + "marker_token": token, + "marker_synonyms": "", + "source_columns": source_columns, + "pro_id": "", + "pro_label": "", + "uniprot_id": uniprot_id, + "uniprot_label": protein_name, + "gene_symbol": approved_symbol, + "hgnc_id": hgnc_id, + "ncbi_gene_id": "", + "mapping_method": "manual", + "confidence": "high" if hgnc_id else "low", + "evidence": evidence, + "notes": GROUP7_NOTES["MR1"], + } + + +# --------------------------------------------------------------------------- # +# Summary +# --------------------------------------------------------------------------- # + + +def print_summary(rows: list[dict[str, str]]) -> None: + """Print a mapping summary to stdout.""" + total = len(rows) + fully_resolved = sum(1 for r in rows if r.get("hgnc_id") and r.get("pro_id")) + gene_only = sum(1 for r in rows if r.get("hgnc_id") and not r.get("pro_id")) + pr_only = sum(1 for r in rows if r.get("pro_id") and not r.get("hgnc_id")) + unresolved = sum(1 for r in rows if not r.get("hgnc_id") and not r.get("pro_id")) + print(f"\nMapping summary ({total} tokens total):") + print(f" Fully resolved (PR + HGNC): {fully_resolved}") + print(f" Gene only (HGNC, no PR): {gene_only}") + print(f" PR only (no HGNC): {pr_only}") + print(f" Unresolved: {unresolved}") + + +# --------------------------------------------------------------------------- # +# Orchestration +# --------------------------------------------------------------------------- # + + +def run( + tokens_path: Path = MARKER_TOKENS_CSV, + tsv_path: Path = CL_PRO_TSV, + output_path: Path = OUTPUT_CSV, + dry_run: bool = False, + session: requests.Session | None = None, + ols4_url: str = OLS4_BASE, + monarch_url: str = MONARCH_URL, + hgnc_url: str = HGNC_REST_URL, + sleep_between: float = 0.2, +) -> list[dict[str, str]]: + """Build the marker-protein-gene mapping and optionally write it to *output_path*. + + Returns the list of output rows regardless of *dry_run*. + """ + sess = session or requests.Session() + + # ------------------------------------------------------------------ # + # Load inputs + # ------------------------------------------------------------------ # + print(f"Loading marker tokens from {tokens_path} ...") + token_rows = load_marker_tokens(tokens_path) + print(f" {len(token_rows)} tokens found.") + + print(f"Loading CL-PRO TSV from {tsv_path} ...") + tsv_rows = load_tsv_rows(tsv_path) + synonym_lookup = build_synonym_lookup(tsv_rows) + print(f" {len(synonym_lookup)} unique CD synonyms indexed.") + + # Build reverse-alias map: canonical CD token → alias token (e.g. CD183 → CXCR3) + alias_reverse: dict[str, str] = {v: k for k, v in ALIAS_MAP.items()} + + # ------------------------------------------------------------------ # + # Resolve each token + # ------------------------------------------------------------------ # + output_rows: list[dict[str, str]] = [] + + # First pass: resolve Group 1 so Group 2 can reference them. + # Always pre-resolve canonical targets for Group 2 aliases even when the + # canonical token is absent from the token list (e.g. in tests). + g1_resolved: dict[str, dict[str, str]] = {} + for alias, canonical in ALIAS_MAP.items(): + if canonical not in g1_resolved: + g1 = resolve_group1(canonical, "", synonym_lookup, alias_reverse) + if g1 is not None: + g1_resolved[canonical] = g1 + + for trow in token_rows: + token = trow["marker_token"] + sc = trow.get("source_columns", "") + if token in ALIAS_MAP: + continue # Group 2 — deferred + g1 = resolve_group1(token, sc, synonym_lookup, alias_reverse) + if g1 is not None: + g1_resolved[token] = g1 + + for trow in token_rows: + token = trow["marker_token"] + sc = trow.get("source_columns", "") + + # -- Group 2: alias tokens ---------------------------------------- + if token in ALIAS_MAP: + row = resolve_group2(token, sc, ALIAS_MAP[token], g1_resolved) + output_rows.append(row) + continue + + # -- Group 1: CD synonyms in TSV ---------------------------------- + if token in g1_resolved: + output_rows.append(g1_resolved[token]) + continue + + # -- Group 3: CD markers needing OLS4 lookup ---------------------- + if token in GROUP3_CONFIG: + print(f" OLS4 lookup for {token!r} ...") + row = resolve_group3( + token, + sc, + GROUP3_CONFIG[token], + sess, + ols4_url=ols4_url, + monarch_url=monarch_url, + sleep_between=sleep_between, + ) + output_rows.append(row) + continue + + # -- Group 4: cytokines ------------------------------------------- + if token in GROUP4_GENE_SYMBOLS: + gene_sym = GROUP4_GENE_SYMBOLS[token] + print(f" HGNC lookup for {token!r} -> {gene_sym} ...") + row = resolve_group4( + token, + sc, + gene_sym, + sess, + hgnc_url=hgnc_url, + sleep_between=sleep_between, + ) + output_rows.append(row) + continue + + # -- Group 5: immunoglobulin classes (manual, no gene) ------------ + if token in GROUP5_NOTES: + row = _empty_row( + token, sc, method="manual", confidence="low", notes=GROUP5_NOTES[token] + ) + output_rows.append(row) + continue + + # -- Group 6: TCR variable region gene-resolved tokens ----------- + if token in TCR_GENE_TOKENS: + imgt_gene = TCR_GENE_TOKENS[token] + extra = TCR_SPECIAL_NOTES.get(token, "") + print(f" HGNC lookup for {token!r} -> {imgt_gene} ...") + row = resolve_group6_gene_token( + token, + sc, + imgt_gene, + extra, + sess, + hgnc_url=hgnc_url, + sleep_between=sleep_between, + ) + output_rows.append(row) + continue + + # -- Group 6: TCR duplicate tokens (copy from primary) ----------- + if token in TCR_DUPLICATE_OF: + primary = TCR_DUPLICATE_OF[token] + # Find the primary's row from output_rows (already appended above) + primary_row = next( + (r for r in output_rows if r["marker_token"] == primary), + None, + ) + if primary_row is not None: + dup_row = dict(primary_row) + dup_row["marker_token"] = token + dup_row["source_columns"] = sc + dup_row["notes"] = TCR_SPECIAL_NOTES.get( + token, f"duplicate of {primary}" + ) + output_rows.append(dup_row) + else: + row = _empty_row( + token, + sc, + method="manual", + confidence="medium", + notes=TCR_SPECIAL_NOTES.get(token, f"duplicate of {primary}"), + ) + output_rows.append(row) + continue + + # -- Group 6: TCR pan-receptor tokens (no gene) ------------------ + if token in TCR_SPECIAL_NOTES: + row = _empty_row( + token, + sc, + method="manual", + confidence="medium", + notes=TCR_SPECIAL_NOTES[token], + ) + output_rows.append(row) + continue + + # -- Group 7: non-protein / complex markers ---------------------- + if token in GROUP7_NOTES: + if token == "MR1": + print(f" HGNC lookup for {token!r} -> MR1 ...") + row = resolve_group7_mr1( + token, + sc, + sess, + hgnc_url=hgnc_url, + sleep_between=sleep_between, + ) + else: + row = _empty_row( + token, + sc, + method="manual", + confidence="low", + notes=GROUP7_NOTES[token], + ) + output_rows.append(row) + continue + + # -- Group 8: parsing artifacts ---------------------------------- + if token in ARTIFACT_TOKENS: + row = _empty_row( + token, + sc, + method="manual", + confidence="low", + notes=( + "likely parsing artifact from multi-word TCR gene name — " + "data quality issue; see reports/marker_validation.md" + ), + ) + output_rows.append(row) + continue + + # -- Unknown token (fallback) ------------------------------------ + row = _empty_row( + token, + sc, + method="manual", + confidence="low", + notes="unclassified token — no mapping strategy defined", + ) + output_rows.append(row) + + # ------------------------------------------------------------------ # + # Output + # ------------------------------------------------------------------ # + print_summary(output_rows) + + if not dry_run: + output_path.parent.mkdir(parents=True, exist_ok=True) + write_csv(output_path, output_rows) + print(f"\nWrote {len(output_rows)} rows to {output_path}.") + + return output_rows + + +# --------------------------------------------------------------------------- # +# CLI +# --------------------------------------------------------------------------- # + + +def main(argv: list[str] | None = None) -> int: + """Entry point for ``soulcap-map``.""" + parser = argparse.ArgumentParser( + prog="soulcap-map", + description="Build marker_mappings/marker_protein_gene.csv.", + ) + parser.add_argument( + "--tokens", + type=Path, + default=MARKER_TOKENS_CSV, + metavar="PATH", + help="Path to marker_tokens.csv (default: marker_mappings/marker_tokens.csv).", + ) + parser.add_argument( + "--tsv", + type=Path, + default=CL_PRO_TSV, + metavar="PATH", + help="Path to cl_pro_relationships.tsv (default: reports/cl_pro_relationships.tsv).", + ) + parser.add_argument( + "--out", + type=Path, + default=OUTPUT_CSV, + metavar="PATH", + help="Output CSV path (default: marker_mappings/marker_protein_gene.csv).", + ) + parser.add_argument( + "--dry-run", + action="store_true", + help="Print summary without writing the output CSV.", + ) + # Internal overrides used in tests + parser.add_argument("--ols4-url", default=OLS4_BASE, help=argparse.SUPPRESS) + parser.add_argument("--monarch-url", default=MONARCH_URL, help=argparse.SUPPRESS) + parser.add_argument("--hgnc-url", default=HGNC_REST_URL, help=argparse.SUPPRESS) + args = parser.parse_args(argv) + + try: + run( + tokens_path=args.tokens, + tsv_path=args.tsv, + output_path=args.out, + dry_run=args.dry_run, + ols4_url=args.ols4_url, + monarch_url=args.monarch_url, + hgnc_url=args.hgnc_url, + ) + except Exception as exc: # noqa: BLE001 + print(f"error: {exc}", file=sys.stderr) + return 1 + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/tests/test_marker_map.py b/tests/test_marker_map.py new file mode 100644 index 0000000..38a96ac --- /dev/null +++ b/tests/test_marker_map.py @@ -0,0 +1,1087 @@ +"""Tests for soulcap_cl_mapping.marker_map. + +All HTTP calls are mocked — these tests never hit OLS4, Monarch, or HGNC. +""" + +from __future__ import annotations + +from pathlib import Path +from unittest.mock import MagicMock, patch + +import pytest + +from soulcap_cl_mapping import marker_map + +# --------------------------------------------------------------------------- # +# Shared mock helpers +# --------------------------------------------------------------------------- # + +MARKER_TOKENS_TSV_CONTENT = ( + "marker_token,source_columns,cell_types\n" + "CD19,Required phenotypic markers,\n" + "CD183,Required phenotypic markers,\n" + "CD8,Required phenotypic markers,\n" + "CCR4,Required phenotypic markers,\n" + "CD57,Required phenotypic markers,\n" + "IFNg,Ideal phenotypic markers,\n" + "IgA,Required phenotypic markers,\n" + "TCRVa24,Required phenotypic markers,\n" + "TCRVa24-Ja18,Required phenotypic markers,\n" + "TCRva24,Required phenotypic markers,\n" + "TCR,Required phenotypic markers,\n" + "Vb11,Required phenotypic markers,\n" + "VB11,Required phenotypic markers,\n" + "Vd1,Required phenotypic markers,\n" + "MR1,Required phenotypic markers,\n" + "Tetramer,Required phenotypic markers,\n" + "CD1d-a-GalCer,Required phenotypic markers,\n" + "V,Required phenotypic markers,\n" + "delta,Required phenotypic markers,\n" +) + +CL_PRO_TSV_CONTENT = ( + "cell\tcell_label\trelation\trelation_label\tsense\tasserted\t" + "pr\tpr_label\tcd_synonym\tuniprot_human\tuniprot_mouse\t" + "xrefs\thgnc_id\thgnc_symbol\n" + "CL:0000236\tB cell\tRO:0002104\thas plasma membrane part\tpositive\tTrue\t" + "PR:000001002\tCD19 molecule\tCD19 (label)\tUniProtKB:P15391\tUniProtKB:P25918\t\tHGNC:1633\tCD19\n" + "CL:0000084\tT cell\tRO:0002104\thas plasma membrane part\tpositive\tTrue\t" + "PR:000001207\tC-X-C chemokine receptor type 3\tCD183 (exact)\tUniProtKB:P49682\t\t\tHGNC:4540\tCXCR3\n" + "CL:0000084\tT cell\tRO:0002104\thas plasma membrane part\tpositive\tTrue\t" + "PR:000001084\tT-cell surface glycoprotein CD8 alpha chain\tCD8 (label); CD8A (exact)\tUniProtKB:P01732\t\t\tHGNC:1706\tCD8A\n" + "CL:0000200\tCD4-positive T cell\tCL:4030046\tlacks_plasma_membrane_part\tnegative\tTrue\t" + "PR:000001200\tC-C chemokine receptor type 4\tCD194 (exact)\tUniProtKB:P51679\t\t\tHGNC:1605\tCCR4\n" +) + + +def _make_mock_response(data: object) -> MagicMock: + resp = MagicMock() + resp.raise_for_status.return_value = None + resp.json.return_value = data + return resp + + +def _make_session(*responses: object) -> MagicMock: + """Return a mock Session whose .get() returns responses in order.""" + session = MagicMock() + if len(responses) == 1: + session.get.return_value = _make_mock_response(responses[0]) + else: + session.get.side_effect = [_make_mock_response(r) for r in responses] + return session + + +# --------------------------------------------------------------------------- # +# parse_cd_synonyms +# --------------------------------------------------------------------------- # + + +def test_parse_cd_synonyms_basic() -> None: + result = marker_map.parse_cd_synonyms("CD19 (label)") + assert result == [("CD19", "label")] + + +def test_parse_cd_synonyms_multiple() -> None: + result = marker_map.parse_cd_synonyms("CD8 (label); CD8A (exact); CD8a (exact)") + assert ("CD8", "label") in result + assert ("CD8A", "exact") in result + + +def test_parse_cd_synonyms_empty() -> None: + assert marker_map.parse_cd_synonyms("") == [] + + +def test_parse_cd_synonyms_no_qualifier() -> None: + result = marker_map.parse_cd_synonyms("CD19") + assert result == [("CD19", "")] + + +# --------------------------------------------------------------------------- # +# build_synonym_lookup +# --------------------------------------------------------------------------- # + + +def _make_tsv_row( + pr: str, + pr_label: str, + cd_synonym: str, + uniprot_human: str, + hgnc_id: str = "", + hgnc_symbol: str = "", +) -> dict[str, str]: + return { + "pr": pr, + "pr_label": pr_label, + "cd_synonym": cd_synonym, + "uniprot_human": uniprot_human, + "hgnc_id": hgnc_id, + "hgnc_symbol": hgnc_symbol, + } + + +def test_build_synonym_lookup_basic() -> None: + rows = [ + _make_tsv_row( + "PR:000001002", + "CD19 molecule", + "CD19 (label)", + "UniProtKB:P15391", + "HGNC:1633", + "CD19", + ) + ] + lookup = marker_map.build_synonym_lookup(rows) + assert "CD19" in lookup + assert lookup["CD19"]["pr"] == "PR:000001002" + + +def test_build_synonym_lookup_label_preferred() -> None: + rows = [ + _make_tsv_row("PR:AAA", "first", "CD33 (exact)", "UniProtKB:PAAA"), + _make_tsv_row("PR:BBB", "second", "CD33 (label)", "UniProtKB:PBBB"), + ] + lookup = marker_map.build_synonym_lookup(rows) + assert lookup["CD33"]["pr"] == "PR:BBB" + + +def test_build_synonym_lookup_hgnc_preferred_over_first() -> None: + rows = [ + _make_tsv_row("PR:AAA", "no_hgnc", "CD99 (exact)", "UniProtKB:P1"), + _make_tsv_row( + "PR:BBB", "has_hgnc", "CD99 (exact)", "UniProtKB:P2", "HGNC:999", "X" + ), + ] + lookup = marker_map.build_synonym_lookup(rows) + assert lookup["CD99"]["pr"] == "PR:BBB" + + +def test_build_synonym_lookup_label_plus_hgnc_beats_label_alone() -> None: + """Canonical entry (label + HGNC) wins over isoform entry (label, no HGNC). + + This guards against CD8 picking an isoform-specific row over the canonical one. + """ + rows = [ + # canonical entry: label + HGNC + _make_tsv_row( + "PR:CANON", + "canonical", + "CD8 (label)", + "UniProtKB:P01732", + "HGNC:1706", + "CD8A", + ), + # isoform entry: label but no HGNC + _make_tsv_row("PR:ISOFORM", "isoform", "CD8 (label)", "UniProtKB:P01732-1"), + ] + lookup = marker_map.build_synonym_lookup(rows) + assert lookup["CD8"]["pr"] == "PR:CANON" + + +def test_build_synonym_lookup_case_insensitive_keys() -> None: + rows = [_make_tsv_row("PR:1", "p", "cd19 (exact)", "UniProtKB:P1")] + lookup = marker_map.build_synonym_lookup(rows) + assert "CD19" in lookup + + +# --------------------------------------------------------------------------- # +# resolve_group1 +# --------------------------------------------------------------------------- # + + +def test_resolve_group1_found() -> None: + rows = [ + _make_tsv_row( + "PR:000001002", + "CD19 molecule", + "CD19 (label)", + "UniProtKB:P15391", + "HGNC:1633", + "CD19", + ) + ] + lookup = marker_map.build_synonym_lookup(rows) + result = marker_map.resolve_group1( + "CD19", "Required phenotypic markers", lookup, {} + ) + assert result is not None + assert result["pro_id"] == "PR:000001002" + assert result["uniprot_id"] == "P15391" + assert result["hgnc_id"] == "HGNC:1633" + assert result["gene_symbol"] == "CD19" + assert result["mapping_method"] == "cl_pro_tsv" + assert result["confidence"] == "high" + + +def test_resolve_group1_not_found() -> None: + lookup: dict = {} + result = marker_map.resolve_group1("CD999", "col", lookup, {}) + assert result is None + + +def test_resolve_group1_adds_alias_synonym() -> None: + rows = [ + _make_tsv_row( + "PR:000001207", + "CXCR3", + "CD183 (exact)", + "UniProtKB:P49682", + "HGNC:4540", + "CXCR3", + ) + ] + lookup = marker_map.build_synonym_lookup(rows) + alias_reverse = {"CD183": "CXCR3"} + result = marker_map.resolve_group1("CD183", "col", lookup, alias_reverse) + assert result is not None + assert "CXCR3" in result["marker_synonyms"] + assert "CD183" in result["marker_synonyms"] + + +def test_resolve_group1_strips_uniprot_prefix() -> None: + rows = [ + _make_tsv_row( + "PR:X", "X protein", "CDTEST (label)", "UniProtKB:P99999; UniProtKB:P88888" + ) + ] + lookup = marker_map.build_synonym_lookup(rows) + result = marker_map.resolve_group1("CDTEST", "col", lookup, {}) + assert result is not None + assert result["uniprot_id"] == "P99999" + + +# --------------------------------------------------------------------------- # +# resolve_group2 +# --------------------------------------------------------------------------- # + + +def test_resolve_group2_copies_g1_data() -> None: + g1_row: dict[str, str] = { + "marker_token": "CD194", + "marker_synonyms": "CCR4|CD194", + "source_columns": "col", + "pro_id": "PR:000001200", + "pro_label": "C-C chemokine receptor type 4", + "uniprot_id": "P51679", + "uniprot_label": "C-C chemokine receptor type 4", + "gene_symbol": "CCR4", + "hgnc_id": "HGNC:1605", + "ncbi_gene_id": "", + "mapping_method": "cl_pro_tsv", + "confidence": "high", + "evidence": "reports/cl_pro_relationships.tsv", + "notes": "", + } + result = marker_map.resolve_group2( + "CCR4", "Required phenotypic markers", "CD194", {"CD194": g1_row} + ) + assert result["marker_token"] == "CCR4" + assert result["pro_id"] == "PR:000001200" + assert result["hgnc_id"] == "HGNC:1605" + assert result["mapping_method"] == "inferred" + assert "CCR4" in result["marker_synonyms"] + assert "CD194" in result["marker_synonyms"] + + +def test_resolve_group2_canonical_not_resolved() -> None: + result = marker_map.resolve_group2("CCR4", "col", "CD194", {}) + assert result["mapping_method"] == "inferred" + assert "not yet resolved" in result["notes"] + + +# --------------------------------------------------------------------------- # +# resolve_group3 +# --------------------------------------------------------------------------- # + +OLS4_CD57_RESPONSE = { + "response": { + "docs": [ + {"obo_id": "PR:000015709", "label": "beta-1,3-glucuronyltransferase 3"} + ] + } +} + +MONARCH_PR_000015709 = { + "PR:000015709": { + "equivalent_identifiers": [ + {"identifier": "HGNC:972", "label": "B3GAT1"}, + {"identifier": "UniProtKB:O43505", "label": "B3GAT1"}, + {"identifier": "NCBIGene:27087", "label": "B3GAT1"}, + ] + } +} + + +def test_resolve_group3_success() -> None: + session = _make_session(OLS4_CD57_RESPONSE, MONARCH_PR_000015709) + result = marker_map.resolve_group3( + "CD57", + "col", + {"query": "CD57", "notes": "B3GAT1"}, + session, + ols4_url="http://ols4", + monarch_url="http://monarch", + sleep_between=0, + ) + assert result["pro_id"] == "PR:000015709" + assert result["gene_symbol"] == "B3GAT1" + assert result["hgnc_id"] == "HGNC:972" + assert result["uniprot_id"] == "O43505" + assert result["mapping_method"] == "ols4" + assert result["confidence"] == "high" + + +def test_resolve_group3_ols4_no_results() -> None: + session = _make_session({"response": {"docs": []}}) + result = marker_map.resolve_group3( + "UNKNOWN", + "col", + {"query": "UNKNOWN", "notes": ""}, + session, + ols4_url="http://ols4", + monarch_url="http://monarch", + sleep_between=0, + ) + assert result["pro_id"] == "" + assert result["confidence"] == "low" + + +def test_resolve_group3_ols4_skips_non_pr() -> None: + session = _make_session( + { + "response": { + "docs": [ + {"obo_id": "CL:0000001", "label": "something"}, + {"obo_id": "PR:000001", "label": "pr term"}, + ] + } + } + ) + result = marker_map.resolve_group3( + "TEST", + "col", + {"query": "TEST", "notes": ""}, + session, + ols4_url="http://ols4", + monarch_url="http://monarch", + sleep_between=0, + ) + # OLS4 found a PR term; Monarch call would fail since session is exhausted + # But fetch_normalized_nodes returns {} for unknown, so it's fine + session.get.side_effect = [ + _make_mock_response( + { + "response": { + "docs": [ + {"obo_id": "CL:0000001", "label": "something"}, + {"obo_id": "PR:000001", "label": "pr term"}, + ] + } + } + ), + _make_mock_response({"PR:000001": None}), + ] + result = marker_map.resolve_group3( + "TEST", + "col", + {"query": "TEST", "notes": ""}, + session, + ols4_url="http://ols4", + monarch_url="http://monarch", + sleep_between=0, + ) + assert result["pro_id"] == "PR:000001" + + +# --------------------------------------------------------------------------- # +# resolve_group4 +# --------------------------------------------------------------------------- # + +HGNC_IFNG_RESPONSE = { + "response": { + "numFound": 1, + "docs": [ + { + "hgnc_id": "HGNC:5438", + "symbol": "IFNG", + "name": "interferon gamma", + "uniprot_ids": ["P01579"], + } + ], + } +} + + +def test_resolve_group4_success() -> None: + session = _make_session(HGNC_IFNG_RESPONSE) + result = marker_map.resolve_group4( + "IFNg", + "col", + "IFNG", + session, + hgnc_url="http://hgnc", + sleep_between=0, + ) + assert result["hgnc_id"] == "HGNC:5438" + assert result["gene_symbol"] == "IFNG" + assert result["uniprot_id"] == "P01579" + assert result["mapping_method"] == "monarch" + assert result["confidence"] == "high" + assert "intracellular" in result["notes"] + + +def test_resolve_group4_not_found() -> None: + session = _make_session({"response": {"numFound": 0, "docs": []}}) + result = marker_map.resolve_group4( + "IFNg", + "col", + "IFNG", + session, + hgnc_url="http://hgnc", + sleep_between=0, + ) + assert result["hgnc_id"] == "" + assert result["confidence"] == "low" + assert result["gene_symbol"] == "IFNG" # falls back to provided symbol + + +def test_resolve_group4_hgnc_id_already_prefixed() -> None: + """hgnc_id in HGNC API already has 'HGNC:' prefix — should not double-prefix.""" + session = _make_session( + { + "response": { + "numFound": 1, + "docs": [ + { + "hgnc_id": "HGNC:5438", # already prefixed + "symbol": "IFNG", + "name": "interferon gamma", + "uniprot_ids": ["P01579"], + } + ], + } + } + ) + result = marker_map.resolve_group4( + "IFNg", + "col", + "IFNG", + session, + hgnc_url="http://hgnc", + sleep_between=0, + ) + # Should be "HGNC:5438", not "HGNC:HGNC:5438" + assert result["hgnc_id"] == "HGNC:5438" + + +# --------------------------------------------------------------------------- # +# resolve_group6_gene_token +# --------------------------------------------------------------------------- # + +HGNC_TRAV10_RESPONSE = { + "response": { + "numFound": 1, + "docs": [ + { + "hgnc_id": "HGNC:12124", + "symbol": "TRAV10", + "name": "T cell receptor alpha variable 10", + "uniprot_ids": [], + } + ], + } +} + + +def test_resolve_group6_gene_token() -> None: + session = _make_session(HGNC_TRAV10_RESPONSE) + result = marker_map.resolve_group6_gene_token( + "TCRVa24", + "col", + "TRAV10", + "Human Vα24 = TRAV10", + session, + hgnc_url="http://hgnc", + sleep_between=0, + ) + assert result["hgnc_id"] == "HGNC:12124" + assert result["gene_symbol"] == "TRAV10" + assert result["mapping_method"] == "manual" + assert result["confidence"] == "medium" + assert "TRAV10" in result["notes"] + + +def test_resolve_group6_gene_token_not_found() -> None: + session = _make_session({"response": {"numFound": 0, "docs": []}}) + result = marker_map.resolve_group6_gene_token( + "TCRVb11", + "col", + "TRBV25-1", + "", + session, + hgnc_url="http://hgnc", + sleep_between=0, + ) + assert result["hgnc_id"] == "" + assert result["gene_symbol"] == "TRBV25-1" + + +# --------------------------------------------------------------------------- # +# resolve_group7_mr1 +# --------------------------------------------------------------------------- # + +HGNC_MR1_RESPONSE = { + "response": { + "numFound": 1, + "docs": [ + { + "hgnc_id": "HGNC:7110", + "symbol": "MR1", + "name": "MHC related 1", + "uniprot_ids": ["Q95460"], + } + ], + } +} + + +def test_resolve_group7_mr1() -> None: + session = _make_session(HGNC_MR1_RESPONSE) + result = marker_map.resolve_group7_mr1( + "MR1", + "col", + session, + hgnc_url="http://hgnc", + sleep_between=0, + ) + assert result["hgnc_id"] == "HGNC:7110" + assert result["gene_symbol"] == "MR1" + assert result["uniprot_id"] == "Q95460" + assert result["mapping_method"] == "manual" + assert "MR1 tetramer" in result["notes"] + + +# --------------------------------------------------------------------------- # +# fetch_hgnc_by_symbol +# --------------------------------------------------------------------------- # + + +def test_fetch_hgnc_by_symbol_success() -> None: + session = _make_session(HGNC_IFNG_RESPONSE) + result = marker_map.fetch_hgnc_by_symbol("IFNG", session, hgnc_url="http://hgnc") + assert result is not None + assert result["hgnc_id"] == "HGNC:5438" + assert result["gene_symbol"] == "IFNG" + assert result["uniprot_id"] == "P01579" + assert result["name"] == "interferon gamma" + + +def test_fetch_hgnc_by_symbol_not_found() -> None: + session = _make_session({"response": {"numFound": 0, "docs": []}}) + result = marker_map.fetch_hgnc_by_symbol("NOTGENE", session, hgnc_url="http://hgnc") + assert result is None + + +def test_fetch_hgnc_by_symbol_http_error() -> None: + session = MagicMock() + resp = MagicMock() + resp.raise_for_status.side_effect = Exception("HTTP 500") + session.get.return_value = resp + with pytest.raises(Exception, match="HTTP 500"): + marker_map.fetch_hgnc_by_symbol("IFNG", session, hgnc_url="http://hgnc") + + +def test_fetch_hgnc_no_uniprot() -> None: + session = _make_session( + { + "response": { + "numFound": 1, + "docs": [ + { + "hgnc_id": "HGNC:12124", + "symbol": "TRAV10", + "name": "T cell receptor alpha variable 10", + # no uniprot_ids key + } + ], + } + } + ) + result = marker_map.fetch_hgnc_by_symbol("TRAV10", session, hgnc_url="http://hgnc") + assert result is not None + assert result["uniprot_id"] == "" + + +# --------------------------------------------------------------------------- # +# search_ols4_pr +# --------------------------------------------------------------------------- # + + +def test_search_ols4_pr_found() -> None: + session = _make_session(OLS4_CD57_RESPONSE) + result = marker_map.search_ols4_pr("CD57", session, ols4_url="http://ols4") + assert result is not None + assert result["pr_id"] == "PR:000015709" + assert "glucuronyltransferase" in result["pr_label"] + + +def test_search_ols4_pr_not_found() -> None: + session = _make_session({"response": {"docs": []}}) + result = marker_map.search_ols4_pr("ZZZNOGENE", session, ols4_url="http://ols4") + assert result is None + + +def test_search_ols4_pr_skips_non_pr_docs() -> None: + session = _make_session( + { + "response": { + "docs": [ + {"obo_id": "GO:0001234", "label": "something"}, + {"obo_id": "PR:000001", "label": "pr term"}, + ] + } + } + ) + result = marker_map.search_ols4_pr("test", session, ols4_url="http://ols4") + assert result is not None + assert result["pr_id"] == "PR:000001" + + +# --------------------------------------------------------------------------- # +# extract_monarch_identifiers +# --------------------------------------------------------------------------- # + + +def test_extract_monarch_identifiers_full() -> None: + node = { + "equivalent_identifiers": [ + {"identifier": "HGNC:972", "label": "B3GAT1"}, + {"identifier": "UniProtKB:O43505", "label": "B3GAT1"}, + {"identifier": "NCBIGene:27087", "label": "B3GAT1"}, + ] + } + result = marker_map.extract_monarch_identifiers(node) + assert result["hgnc_id"] == "HGNC:972" + assert result["gene_symbol"] == "B3GAT1" + assert result["uniprot_id"] == "O43505" + assert result["ncbi_gene_id"] == "27087" + + +def test_extract_monarch_identifiers_skips_isoform_uniprot() -> None: + node = { + "equivalent_identifiers": [ + {"identifier": "UniProtKB:O43505-1", "label": ""}, + {"identifier": "UniProtKB:O43505", "label": ""}, + ] + } + result = marker_map.extract_monarch_identifiers(node) + # Isoform O43505-1 should be skipped; canonical O43505 should be picked + assert result["uniprot_id"] == "O43505" + + +def test_extract_monarch_identifiers_empty_node() -> None: + result = marker_map.extract_monarch_identifiers({}) + assert result == { + "hgnc_id": "", + "gene_symbol": "", + "uniprot_id": "", + "ncbi_gene_id": "", + } + + +# --------------------------------------------------------------------------- # +# print_summary +# --------------------------------------------------------------------------- # + + +def test_print_summary(capsys: pytest.CaptureFixture) -> None: + rows = [ + {"hgnc_id": "HGNC:1", "pro_id": "PR:1"}, # fully resolved + {"hgnc_id": "HGNC:2", "pro_id": ""}, # gene only + {"hgnc_id": "", "pro_id": "PR:2"}, # pr only + {"hgnc_id": "", "pro_id": ""}, # unresolved + ] + marker_map.print_summary(rows) + out = capsys.readouterr().out + assert "4 tokens total" in out + assert "Fully resolved" in out + assert "Gene only" in out + assert "PR only" in out + assert "Unresolved" in out + + +# --------------------------------------------------------------------------- # +# load_marker_tokens / load_tsv_rows / write_csv +# --------------------------------------------------------------------------- # + + +def test_load_marker_tokens(tmp_path: Path) -> None: + p = tmp_path / "tokens.csv" + p.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + rows = marker_map.load_marker_tokens(p) + assert len(rows) == 19 + assert rows[0]["marker_token"] == "CD19" + + +def test_load_tsv_rows(tmp_path: Path) -> None: + p = tmp_path / "cl.tsv" + p.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + rows = marker_map.load_tsv_rows(p) + assert len(rows) == 4 + assert rows[0]["pr"] == "PR:000001002" + + +def test_write_csv(tmp_path: Path) -> None: + p = tmp_path / "out.csv" + rows = [{f: "" for f in marker_map.OUTPUT_FIELDS}] + rows[0]["marker_token"] = "CD19" + rows[0]["pro_id"] = "PR:000001002" + marker_map.write_csv(p, rows) + content = p.read_text(encoding="utf-8") + assert "marker_token" in content + assert "CD19" in content + assert "PR:000001002" in content + + +# --------------------------------------------------------------------------- # +# run() — integration with mocked HTTP +# --------------------------------------------------------------------------- # + + +def _build_mock_session_for_run() -> MagicMock: + """Build a session that responds to the API calls made during run() for the + minimal test token set in MARKER_TOKENS_TSV_CONTENT.""" + # Calls made: + # 1. OLS4 search for "CD57" (Group 3) + # 2. Monarch lookup for PR:000015709 (Group 3) + # 3. HGNC lookup for IFNG (Group 4) + # 4. HGNC lookup for TRAV10 (Group 6 — TCRVa24) + # 5. HGNC lookup for TRAV10 again for TCRva24 duplicate (no call — copy) + # 6. HGNC lookup for TRBV25-1 (Vb11 / VB11 / TCRVb11 not in our minimal token list) + # 7. HGNC lookup for TRDV1 (Vd1 — Group 6) + # 8. HGNC lookup for MR1 (Group 7) + session = MagicMock() + session.get.side_effect = [ + _make_mock_response(OLS4_CD57_RESPONSE), # CD57 OLS4 + _make_mock_response(MONARCH_PR_000015709), # CD57 Monarch + _make_mock_response(HGNC_IFNG_RESPONSE), # IFNg + _make_mock_response(HGNC_TRAV10_RESPONSE), # TCRVa24 + _make_mock_response( + { # Vd1 → TRDV1 + "response": { + "numFound": 1, + "docs": [ + { + "hgnc_id": "HGNC:12202", + "symbol": "TRDV1", + "name": "T cell receptor delta variable 1", + "uniprot_ids": [], + } + ], + } + } + ), + _make_mock_response(HGNC_MR1_RESPONSE), # MR1 + ] + return session + + +def test_run_returns_correct_row_count(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + rows = marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=tmp_path / "out.csv", + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + # Must return one row per input token + assert len(rows) == 19 + + +def test_run_group1_resolved(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + rows = marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=tmp_path / "out.csv", + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + by_token = {r["marker_token"]: r for r in rows} + # CD19 is in the CL-PRO TSV + cd19 = by_token["CD19"] + assert cd19["pro_id"] == "PR:000001002" + assert cd19["uniprot_id"] == "P15391" + assert cd19["mapping_method"] == "cl_pro_tsv" + assert cd19["confidence"] == "high" + + +def test_run_group2_alias_resolved(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + rows = marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=tmp_path / "out.csv", + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + by_token = {r["marker_token"]: r for r in rows} + # CCR4 maps to CD194 which is in the CL-PRO TSV + ccr4 = by_token["CCR4"] + assert ccr4["mapping_method"] == "inferred" + assert ccr4["pro_id"] == "PR:000001200" + assert "CCR4" in ccr4["marker_synonyms"] + + +def test_run_group3_cd57(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + rows = marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=tmp_path / "out.csv", + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + by_token = {r["marker_token"]: r for r in rows} + cd57 = by_token["CD57"] + assert cd57["pro_id"] == "PR:000015709" + assert cd57["hgnc_id"] == "HGNC:972" + assert cd57["mapping_method"] == "ols4" + + +def test_run_group4_ifng(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + rows = marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=tmp_path / "out.csv", + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + by_token = {r["marker_token"]: r for r in rows} + ifng = by_token["IFNg"] + assert ifng["gene_symbol"] == "IFNG" + assert ifng["hgnc_id"] == "HGNC:5438" + assert ifng["mapping_method"] == "monarch" + assert "intracellular" in ifng["notes"] + + +def test_run_group5_iga(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + rows = marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=tmp_path / "out.csv", + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + by_token = {r["marker_token"]: r for r in rows} + iga = by_token["IgA"] + assert iga["pro_id"] == "" + assert iga["hgnc_id"] == "" + assert iga["mapping_method"] == "manual" + assert iga["confidence"] == "low" + assert "IGHA" in iga["notes"] + + +def test_run_group6_tcr_duplicate(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + rows = marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=tmp_path / "out.csv", + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + by_token = {r["marker_token"]: r for r in rows} + # TCRva24 is a duplicate of TCRVa24 (different capitalisation) + tcrva24 = by_token.get("TCRva24") + assert tcrva24 is not None + assert "duplicate" in tcrva24["notes"].lower() + + +def test_run_group8_artifact(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + rows = marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=tmp_path / "out.csv", + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + by_token = {r["marker_token"]: r for r in rows} + v = by_token["V"] + assert v["pro_id"] == "" + assert "parsing artifact" in v["notes"] + assert v["mapping_method"] == "manual" + assert v["confidence"] == "low" + + +def test_run_writes_csv(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + out_csv = tmp_path / "out.csv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=out_csv, + dry_run=False, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + assert out_csv.exists() + content = out_csv.read_text(encoding="utf-8") + assert "marker_token" in content + assert "CD19" in content + + +def test_run_dry_run_no_write(tmp_path: Path) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + out_csv = tmp_path / "out.csv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + marker_map.run( + tokens_path=tokens_csv, + tsv_path=tsv_csv, + output_path=out_csv, + dry_run=True, + session=session, + ols4_url="http://ols4", + monarch_url="http://monarch", + hgnc_url="http://hgnc", + sleep_between=0, + ) + assert not out_csv.exists() + + +# --------------------------------------------------------------------------- # +# main() — CLI +# --------------------------------------------------------------------------- # + + +def test_main_dry_run(tmp_path: Path, capsys: pytest.CaptureFixture) -> None: + tokens_csv = tmp_path / "tokens.csv" + tsv_csv = tmp_path / "cl.tsv" + tokens_csv.write_text(MARKER_TOKENS_TSV_CONTENT, encoding="utf-8") + tsv_csv.write_text(CL_PRO_TSV_CONTENT, encoding="utf-8") + + session = _build_mock_session_for_run() + with patch("soulcap_cl_mapping.marker_map.requests.Session", return_value=session): + rc = marker_map.main( + [ + "--tokens", + str(tokens_csv), + "--tsv", + str(tsv_csv), + "--dry-run", + "--ols4-url", + "http://ols4", + "--monarch-url", + "http://monarch", + "--hgnc-url", + "http://hgnc", + ] + ) + assert rc == 0 + + +def test_main_missing_tokens_file(tmp_path: Path) -> None: + rc = marker_map.main( + [ + "--tokens", + str(tmp_path / "nonexistent.csv"), + "--tsv", + str(tmp_path / "cl.tsv"), + ] + ) + assert rc == 1 + + +def test_main_constant_paths() -> None: + """Ensure default path constants point to correct locations.""" + assert marker_map.MARKER_TOKENS_CSV.name == "marker_tokens.csv" + assert marker_map.MARKER_TOKENS_CSV.parent.name == "marker_mappings" + assert marker_map.CL_PRO_TSV.name == "cl_pro_relationships.tsv" + assert marker_map.OUTPUT_CSV.name == "marker_protein_gene.csv" From da183b12bfe5f3dfba93f9ebc24757be265d6a83 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Wed, 15 Jul 2026 16:22:59 -0400 Subject: [PATCH 3/8] =?UTF-8?q?feat:=20Milestone=202=20=E2=80=94=20NK=20ce?= =?UTF-8?q?ll=20marker=20literature=20report?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Add reports/literature/nk_cell_markers.md with verbatim-quoted evidence for all 10 NK cell markers used in SOULCAP (CD56+, CD3-, CD19-, CD14-, CD127-, CD16, CD57, HLA-DR, CD11c, CD56bright/dim subsets), drawn from 3 open-access papers (Rebuffet 2024 Nat Immunol, Scoville 2017 Front Immunol, Van Acker 2017 Front Immunol). Two paywalled papers (Vivier 2024 Nature, Aranami 2006 J Immunol) noted as not accessed. Key finding: CD127 and HLA-DR caveated as ideal rather than required exclusions based on the evidence. Co-Authored-By: Claude Sonnet 4.6 --- reports/literature/nk_cell_markers.md | 175 ++++++++++++++++++++++++++ 1 file changed, 175 insertions(+) create mode 100644 reports/literature/nk_cell_markers.md diff --git a/reports/literature/nk_cell_markers.md b/reports/literature/nk_cell_markers.md new file mode 100644 index 0000000..3eccf00 --- /dev/null +++ b/reports/literature/nk_cell_markers.md @@ -0,0 +1,175 @@ +# NK Cell Marker Literature Support + +Evidence for SOULCAP NK cell marker definitions, extracted verbatim from three open-access papers. +Two papers (Vivier 2024 Nature PMID:38383621; Aranami 2006 J Immunol PMID:17015755) are paywalled and could not be accessed. + +--- + +## Markers with evidence + +### CD56 (positive marker) + +NK cells are canonically defined by surface CD56 expression. CD56 is the 140-kDa isoform of the neural cell adhesion molecule (NCAM). + +> "Natural killer cells are prototypic members of the innate lymphoid cell (ILC) family and characterized in humans by expression of the phenotypic marker CD56 in the absence of CD3." +— Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) + +> "human NK cells are typically divided into two main categories on the basis of the density of CD56, the 140-kDa isoform of the neural cell adhesion molecule (NCAM)2, on the cell surface: CD56bright and CD56dim NK cells." +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +--- + +### CD3 (exclusion marker) + +NK cells lack CD3 surface expression; this distinguishes them from T cells and is part of the standard lineage-exclusion gate used to identify ILCs including NK cells. + +> "Natural killer cells are prototypic members of the innate lymphoid cell (ILC) family and characterized in humans by expression of the phenotypic marker CD56 in the absence of CD3." +— Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) + +> "ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303)." +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +The CD56-negative NK cell subpopulation is explicitly defined by CD3 absence: + +> "there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes" +— Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) + +--- + +### CD19 (exclusion marker) + +CD19 marks B cells and is excluded from the NK cell lineage gate. + +> "ILCs lack expression of markers specific for other leukocytes, including antigen-specific T and B cell receptors (i.e., CD3/TCR and CD19/BCR)." +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +> "ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303)." +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +The CD56-negative NK cell subpopulation definition also uses CD19 exclusion: + +> "there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes" +— Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) + +--- + +### CD14 (exclusion marker) + +CD14 marks monocytes and is excluded from the NK cell lineage gate. + +> "ILCs are identified as “lineage” (Lin) negative lymphocytes, lacking expression of surface markers more specifically expressed on T cells (CD3, CD5, TCR), B cells (CD19, CD20, BCR), myelomonocytic cells (CD14, CD15, CD36), and dendritic cells (DCs) (CD116, CD123, CD303)." +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +> "there also exists a CD56− NK cell subpopulation, namely CD3−CD4−CD14−CD19−CD16+NKp46+ lymphocytes" +— Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) + +--- + +### CD127 / IL-7Rα (negative or low on mature NK cells) + +CD127 (IL-7Rα) is expressed on all non-NK innate lymphoid cells (ILC1, ILC2, ILC3) and is used to distinguish mature NK cells from other ILCs. NK cells can express low levels of CD127, but it is a characteristic marker of non-NK ILCs rather than NK cells. + +> "In humans, all non-NK ILCs express CD127 (IL-7Rα) and CD161 (NKRP1A) (13–16), and they may be further distinguished according to the expression of other subset-associated surface antigens including CXCR3, CD294 (CRTH2), and CD117 (c-Kit) for ILC1s, ILC2s, and ILC3s, respectively (10, 17). Human NK cells can also express the pan-ILC markers CD127 and CD161 (18–20), but NK cells are typically distinguished by their surface expression of CD16 (FcγRIIIA), CD94/NKG2 heterodimers, killer immunoglobulin-like receptors (KIRs), NKG2D, and NKp80 (21)." +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +CD127 expression also distinguishes NK cell progenitors from ILC3 precursors in secondary lymphoid tissues: + +> "They demonstrated that a minute CD127− fraction preferentially gave rise to NK cells whereas the predominant CD127+ fraction mostly retained ILC3 features. Thus CD127 has since been touted as a critical marker distinguishing human stage 3 NK cell precursors from ILC3s" +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +*Note:* These papers confirm that non-NK ILCs reliably express CD127 while mature NK cells typically do not. The CD127-low/negative phenotype of mature NK cells supports its use as a lineage-exclusion marker for ILC contamination, though the cited passages describe NK cells as variably expressing CD127 rather than being uniformly CD127-negative. Use of CD127- as a required exclusion warrants caution. + +--- + +### CD56bright vs CD56dim subsets + +The existence and phenotypic properties of two major NK cell subsets defined by CD56 density are firmly established. + +> "They are usually further divided into two subsets based on their surface level expression of CD56 (3). Whereas most NK cells in peripheral blood are CD56dim, CD56bright NK cells are more abundant in tissues." +— Van Acker HH et al. 2017 (PMID:28791027; DOI:10.3389/fimmu.2017.00892) + +> "Two subsets of human peripheral blood (PB) NK cells can be distinguished according to their relative expression of the pan-NK cell surface marker, CD56 (NCAM-1): “CD56bright” and “CD56dim” (22, 23). CD56bright human NK cells express high levels of CD62L (l-selectin) and CD94 but absent or low levels of CD16 and KIRs; they predominate in secondary lymphoid tissues (SLTs) such as lymph nodes (LNs) and tonsils; they show low baseline perforin expression and cytotoxic activity ex vivo; and they rapidly produce cytokines, including IFN-γ, following stimulation by monocyte-derived cytokines (“monokines”), such as IL-12, IL-15, and IL-18 (22). In contrast, CD56dim NK cells are CD16hi and express more KIRs but less CD94 and CD62L; they predominate in PB; they show high baseline perforin expression and cytotoxicity against MHC class I negative target cells; and they preferentially produce cytokines in response to direct target cell interactions rather than via monokine stimulation (3)." +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +High-dimensional CITE-seq and scRNA-seq analysis confirms the CD56bright/dim dichotomy corresponds to the NK2 and NK1 major clusters: + +> "The NK2 cluster was defined by high expression of CD56, CD27, CD44, CD54, CD45RB, CD314 (NKG2D) and CD335 (NKp46) and little or no expression of CD16 and CD57 at the protein level (Fig. 1c,d)." +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +--- + +### CD16 (expressed on CD56dim NK cells; absent/low on CD56bright) + +CD16 (FcγRIIIA) is a key NK cell marker expressed at high levels on the dominant peripheral blood CD56dim subset. + +> "NK cells are typically distinguished by their surface expression of CD16 (FcγRIIIA), CD94/NKG2 heterodimers, killer immunoglobulin-like receptors (KIRs), NKG2D, and NKp80 (21)." +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +> "The NK1 cluster was marked by high protein expression of CD16, CX3CR1, CD161, β7-integrin and CD38 (Fig. 1c,d)." +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +> "Expression of the classic NK cell markers CD57 and CD16 was reduced or absent on NK2 cells compared with NK1 and NK3 cells, indicating that the NK2 population comprised CD56bright and early-stage CD56dim NK cells." +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +--- + +### CD57 (positive marker for mature NK subsets) + +CD57 marks terminally differentiated, mature NK cells within the CD56dim compartment. + +> "Further distinctions in the CD56dim population are made on the basis of expression of the CD57 carbohydrate moiety3 on the cell surface and the absence of CD94–NKG2A and CD62L; cells with these features comprise a more mature subset4–7." +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +> "this cluster's preferential expression of CD57 and PRDM1 suggests that it also includes mature CD57+CD56dim NK cells that are not produced in response to HCMV." +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +> "some that were NKp80+CD16+ and coexpressed KIRs and CD57, the latter of which has been associated with terminal maturation and may represent a putative “stage 6” of human NK cell development" +— Scoville SD et al. 2017 (PMID:28396671; DOI:10.3389/fimmu.2017.00360) + +--- + +### HLA-DR (ideal exclusion; expressed on a subset of NK cells) + +HLA-DR expression is not a universal feature of NK cells, but a subset of adaptive/HCMV-associated NK cells does express HLA-D-family genes, motivating its use as an ideal (non-required) exclusion marker in gating. + +> "Notably, NK3B (cluster 1) was distinguished by expression of members of the HLA-D gene family, CD74, CCL5, CD7 and KLRC1, and NK3A exhibited enhanced cytotoxic capabilities (through expression of GZMA, GZMB and PRF1)" +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +*Note:* No passage in any of the three papers explicitly states that canonical NK cells are HLA-DR-negative. Van Acker et al. mention HLA-DR only as a generic activation marker comparable to CD69. The Rebuffet finding that a subset of adaptive NK cells (NK3B) expresses HLA-D family genes is the strongest available evidence from these papers that HLA-DR can be found on NK cells, which is why it is used as an ideal (not required) exclusion. + +--- + +### CD11c (expressed on NK2 / CD56bright subset) + +CD11c (ITGAX, integrin alpha X) shows differential expression across NK cell subsets, being more pronounced on NK2 (CD56bright-enriched) cells. + +> "CD11C (ITGAX) expression was more pronounced in NK2." +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +Full context: + +> "Activation markers also served as differential markers, with CD69 being most prominent in NK1B and NKint, whereas TNFRSF18 (encoding GITR) was more pronounced in NK2. Moreover, classic markers of NK maturation aligned with earlier descriptions: CD56 (NCAM1) was more prevalent in NK2, and CD16 (FCGR3A) expression increased progressively from NK2 to NK1C. In addition, CD11B (ITGAM) levels were higher in NK1B, whereas CD11C (ITGAX) expression was more pronounced in NK2." +— Rebuffet L et al. 2024 (PMID:38956378; DOI:10.1038/s41590-024-01883-0) + +*Note:* CD11c expression in NK cells is subset-specific. CD56bright NK cells (NK2) preferentially express CD11c; NK cells are not uniformly CD11c-negative. This supports using CD11c as an ideal exclusion rather than a required one — strict application as CD11c- would exclude CD56bright NK cells. + +--- + +## Markers with no direct evidence found in these three papers + +None of the ten SOULCAP markers listed above were completely absent from the three papers; all had at least indirect supporting evidence. However, the following caveats apply: + +- **CD127 (required negative):** These papers show mature NK cells can variably express CD127; the "non-NK ILCs reliably express CD127" framing is clearer than "NK cells are CD127-negative." Direct evidence for mature peripheral blood NK cells being CD127-negative is not provided verbatim in any of these three papers. +- **HLA-DR (ideal exclusion):** No passage explicitly states that canonical NK cells are HLA-DR-negative. The Rebuffet NK3B finding shows a subset expresses HLA-D family genes, but this is transcriptomic data for an adaptive NK subset. + +--- + +## Sources + +| PMID | DOI | Title | Authors | Year | Access | +|------|-----|-------|---------|------|--------| +| 38956378 | 10.1038/s41590-024-01883-0 | High-dimensional single-cell analysis of human natural killer cell heterogeneity | Rebuffet L et al. | 2024 | Open access | +| 28396671 | 10.3389/fimmu.2017.00360 | Modeling Human Natural Killer Cell Development in the Era of Innate Lymphoid Cells | Scoville SD et al. | 2017 | Open access | +| 28791027 | 10.3389/fimmu.2017.00892 | CD56 in the Immune System: More Than a Marker for Cytotoxicity? | Van Acker HH et al. | 2017 | Open access | +| 38383621 | 10.1038/s41586-023-06945-1 | Natural killer cell therapies | Vivier E et al. | 2024 | Paywalled — not accessed | +| 17015755 | 10.4049/jimmunol.177.8.5659 | Differential expression of CD11c by peripheral blood NK cells reflects temporal activity of multiple sclerosis | Aranami T et al. | 2006 | Paywalled — not accessed | From 422d7aa63f16df77282babad047870e484b41396 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Thu, 16 Jul 2026 16:53:31 -0400 Subject: [PATCH 4/8] =?UTF-8?q?feat:=20Milestone=202=20=E2=80=94=20ILC,=20?= =?UTF-8?q?DC,=20iNKT,=20and=20T=20cell=20marker=20literature=20reports?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Four new verbatim-quote reports under reports/literature/: - ilc_markers.md — 4 open-access papers (Krabbendam 2021, Alkon 2022, Bonne-Année 2019, Bento 2025); covers CD127, CD3, CD161, CD294/CRTH2, CD117/c-Kit, CD56, and lineage-exclusion markers - dc_markers.md — 3 open-access papers (Rhodes 2019, Villani 2017, Guilliams 2016); covers CD11c, HLA-DR, CD1c, CD141, CD172a/SIRPα, FceR1a, CD123, CD303, CD33, CD64, CD14/CD16, and Lin dump - inkt_markers.md — 2 open-access papers (Lal 2018 OMIP-046, Zhou 2022); covers CD3, TCRVα24-Jα18, TCRVβ11, CD1d pentamer; also documents the iNKT vs Type II NKT distinction relevant to CL issue #13 - t_cell_markers.md — 12 open-access sources; covers CD3, CD4/CD8, TCRαβ/TCRγδ, CXCR3/CD183, CXCR5/CD185, CCR4/CD194, CCR6/CD196, CRTH2/CD294, CD25+CD127lo (Treg), CD45RA+CCR7, CD27+CD28 Co-Authored-By: Claude Sonnet 4.6 --- reports/literature/dc_markers.md | 320 +++++++++++++++++++++++ reports/literature/ilc_markers.md | 176 +++++++++++++ reports/literature/inkt_markers.md | 182 +++++++++++++ reports/literature/t_cell_markers.md | 369 +++++++++++++++++++++++++++ 4 files changed, 1047 insertions(+) create mode 100644 reports/literature/dc_markers.md create mode 100644 reports/literature/ilc_markers.md create mode 100644 reports/literature/inkt_markers.md create mode 100644 reports/literature/t_cell_markers.md diff --git a/reports/literature/dc_markers.md b/reports/literature/dc_markers.md new file mode 100644 index 0000000..c111c2e --- /dev/null +++ b/reports/literature/dc_markers.md @@ -0,0 +1,320 @@ +# DC Marker Literature Support + +Evidence for SOULCAP dendritic cell (DC) marker definitions, extracted verbatim from +open-access papers. Paywalled papers are noted in the Sources table but not quoted. + +All block-quoted text was copied verbatim from the fetched page content; no paraphrasing +has been applied. Table-cell values from Table 1 of Rhodes et al. are reproduced +exactly as they appear in the published table. + +--- + +## Markers with evidence + +### CD11c / ITGAX (required high on cDC; low on pDC) + +Biological context: CD11c (integrin alpha X, encoded by *ITGAX*) is the classical +surface marker of conventional DCs. cDCs express CD11c at high levels; pDCs are +CD11c-low or negative. SOULCAP requires CD11chi on all cDC gates and uses CD11clo +to help identify pDC. + +> "Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123−" + +— Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) + +> "pDCs are CD11c− CD123+ cells best characterized for their type I interferon" + +— Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) + +> "CD11c, a 'classical' cDC marker, can be downregulated on DCs" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +> "human pDCs (defined as CD45+CD11cloHLADRhi cells) were IRF8hiIRF4int across tissues" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +> "For DCs, we sampled LIN−HLA-DR+CD14− cells across the CD11C+ fraction (to enrich for +> CD141+ and CD1C+ cDCs) and the CD11C− fraction" + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +--- + +### HLA-DR / MHC class II (required positive on all DC subsets) + +Biological context: HLA-DR (MHC class II) is expressed at high levels on all mature +human DCs and is used as a pan-DC positive selection marker in combination with lineage +exclusion. + +> "DCs were defined as live, LIN(CD3, CD19, CD56)−CD14−HLA-DR+ cells." + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +> "Numerous studies have shown that human dendritic cells express high levels of major +> histocompatibility complex (MHC) class II (e.g., HLA-DR)" + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +> "human pDCs (defined as CD45+CD11cloHLADRhi cells)" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +Note: In Table 1 of Rhodes et al. 2019, cDC2-A entries show HLA-DR as "HLA-DR++", +while pDC entries show "HLA-DRlo", confirming differential expression across subsets. + +--- + +### CD1c / BDCA-1 (cDC2 positive; cDC1 negative) + +Biological context: CD1c (also called BDCA-1) is the canonical positive marker for +cDC2 (the most abundant blood cDC). cDC1s do not express CD1c. + +> "DC2 and DC3 correspond to new subdivisions of the CD1C/BDCA-1+ cDC2" + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +> "Although both cDC2 subsets can be characterized by CD1c expression, cDC2-A (CD32b+) +> are distinguished" + +— Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) + +> "CD172ahiCD1chi cDC2s" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +> "In the blood, DC subtypes include CD11C+ conventional DCs (cDCs), consisting of +> either CD141+ or CD1C+ cells" + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +--- + +### CD141 / BDCA-3 / Thrombomodulin (cDC1 positive marker; lo/− on cDC2) + +Biological context: CD141 (BDCA-3, thrombomodulin) defines the cross-presenting cDC1 +subset in human blood. cDC2s express low or absent CD141. + +> "DC1 corresponds to the cross-presenting CD141/BDCA-3+ cDC1, which is best marked +> by CLEC9A" + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +> "cDC1s can be best identified by expression of C-type lectin-like receptor (Clec)9A +> and cell adhesion molecule 1 (CADM1)...and also express high levels of CD141 and XCR1" + +— Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) + +--- + +### CD172a / SIRPα (ideal positive on cDC2; negative on cDC1) + +Biological context: CD172a (signal regulatory protein alpha, SIRPα) marks cDC2 and +is absent from cDC1. It is used in combination with CD1c and CADM1/XCR1 to cleanly +separate the two cDC lineages. + +> "using CADM1 or XCR1 in combination with CD172a to separate cDC1s from cDC2s" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +> "CD172ahiCD1chi cDC2s" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +Rhodes et al. 2019 Table 1 (verbatim table-cell values by subset): + +| DC subset | SIRPα (CD172a) | +|-----------|----------------| +| cDC1 | SIRPα− | +| cDC2-A | SIRPα+ | +| cDC2-B | SIRPα+ | + +— Rhodes JW et al. 2019, Table 1 (DOI:10.3389/fimmu.2019.01088) + +--- + +### FceR1a / FCER1A (ideal positive on cDC2; also on basophils — see CD193) + +Biological context: FcεRI (the high-affinity IgE receptor alpha chain, FCER1A) is +expressed on cDC2s, where it was found as a unique transcript marker of the CD1c+ DC +population. It is also expressed on basophils, which must be excluded separately (see +CD193/CCR3 below). + +> "CD1C+ DCs (DC2 and DC3) expressed unique markers (e.g. CD1C, CLEC10A, FCER1A, +> FCGR2B, and CD1D" + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +Note: This quote lists *FCER1A* as a gene-level marker of CD1c+ DCs (cDC2 lineage), +consistent with its use as a phenotypic marker in SOULCAP. Because FceR1a is also +present on basophils, SOULCAP employs CD193 (CCR3) or CD303 to exclude basophils +from the cDC2 gate. + +--- + +### CD123 / IL-3Rα (high on pDC; low/negative on cDC) + +Biological context: CD123 (IL-3 receptor alpha chain) is expressed at high levels on +pDCs, in contrast to the CD123-low/negative expression seen on cDCs. It is therefore +used both to positively select pDCs and to exclude basophils (which also express CD123 +at high levels, hence the additional CD303 criterion in SOULCAP). + +> "Conventional DCs (cDCs), also known as myeloid DCs, can be defined as CD11c+ CD123−" + +— Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) + +> "pDCs are CD11c− CD123+ cells best characterized for their type I interferon" + +— Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) + +> "Traditionally defined as CD123+ BDCA-2+ cells, pDCs have also been redefined by +> single-cell RNA sequencing" + +— Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) + +> "plasmacytoid DCs (pDCs), consisting of CD123+ cells" + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +--- + +### CD303 / BDCA-2 / CLEC4C (pDC marker) + +Biological context: CD303 (BDCA-2, CLEC4C) is a C-type lectin receptor expressed +selectively on pDCs. Together with CD123, it forms the canonical two-marker pDC +definition and distinguishes pDCs from basophils (which are CD123-high but CD303-low). + +> "pDCs (e.g. IL3RA/CD123, CLEC4C/CD303)" + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +> "Traditionally defined as CD123+ BDCA-2+ cells, pDCs" + +— Rhodes JW et al. 2019 (DOI:10.3389/fimmu.2019.01088) + +> "CD123hiCD303hi (human) pDCs" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +--- + +### CD33 / SIGLEC3 (high on cDC; negative on pDC — used to distinguish) + +Biological context: CD33 (Siglec-3) is a myeloid surface antigen expressed at high +levels on cDCs and intermediate levels on some DC3/DC4 subsets, but absent from pDCs. +SOULCAP uses (CD33hi|CD64+) as an inclusive criterion to positively select cDCs while +allowing either marker to qualify. + +Rhodes et al. 2019 Table 1 (verbatim table-cell values by subset): + +| DC subset | CD33 | +|------------|----------| +| cDC1 | CD33+ | +| cDC2-A | CD33+ | +| cDC2-B | CD33+ | +| CD16+ DC | CD33int | +| Axl+ DC | CD33int | +| pDC | CD33− | + +— Rhodes JW et al. 2019, Table 1 (DOI:10.3389/fimmu.2019.01088) + +Note: The table shows CD33 as positive on all cDC subsets and negative on pDC, +supporting its utility as a myeloid/cDC-enriching marker in the (CD33hi|CD64+) gate. + +--- + +### CD64 / FcγRI / FCGR1A (optional positive for cDC; shared with macrophages) + +Biological context: CD64 (FcγRI) was historically considered a macrophage-restricted +marker, but published evidence shows that cDCs also express CD64 at detectable levels, +making it unsuitable as a negative marker to exclude macrophages from the DC gate — +and conversely supporting its use in SOULCAP as part of an inclusive OR gate +(CD33hi|CD64+) for cDC identification. + +> "In human and macaque, CD64 cannot be used, as cDCs also express some CD64." + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +> "CD64 is highly expressed on Macs" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +Note: The first quote confirms that cDC expression of CD64 is a documented fact +rather than contamination. SOULCAP exploits this by using CD64 positivity as an +alternative to high CD33 to capture cDCs; macrophage contamination is controlled by +the CD11chi HLA-DR+ requirement together with CD14−/CD16− exclusion. + +--- + +### CD14 and CD16 (exclusion markers on cDC and pDC gates) + +Biological context: CD14 and CD16 are classical monocyte surface markers. Their +exclusion from the DC gate is essential to prevent monocyte contamination. CD16 (FCGR3A) +marks a discrete DC4 population in some classification schemes but is excluded in +the SOULCAP cDC and pDC definitions. + +> "DCs were defined as live, LIN(CD3, CD19, CD56)−CD14−HLA-DR+ cells." + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +> "CD14loCD16lo in human and macaque" + +— Guilliams M et al. 2016 (PMID:27637149; DOI:10.1016/j.immuni.2016.08.057) + +Note: The Guilliams quote describes the CD14loCD16lo criterion applied when gating +non-macrophage DCs in human blood and tissue, confirming the exclusion strategy. + +Additionally, Villani et al. 2017 identify a separate DC4 population marked by CD16: + +> "The DC4 cluster mapped to the CD141−CD1C− population and was accurately delineated +> by FCGR3A/CD16." + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +This population (DC4/CD16+ DC) is excluded from the SOULCAP cDC, cDC1, and cDC2 +definitions by the CD16− requirement, consistent with its distinct transcriptional +profile. + +--- + +### CD3 / CD19 / CD56 / CD127 (lineage exclusion panel) + +Biological context: The standard "lineage dump" removes T cells (CD3), B cells (CD19), +NK cells (CD56), and ILC/lymphocyte progenitors (CD127) before gating DCs, preventing +cross-contamination from non-DC populations. + +> "DCs were defined as live, LIN(CD3, CD19, CD56)−CD14−HLA-DR+ cells." + +— Villani AC et al. 2017 (PMID:28428369; DOI:10.1126/science.aah4573) + +Note: The SOULCAP pDC gate additionally requires CD127− (IL-7Rα) to exclude ILCs and +plasmacytoid-like lymphoid progenitors, which Villani et al. do not include in this +specific gating line but which is established practice for pure pDC isolation. + +--- + +## Markers with no direct evidence found + +### CD193 / CCR3 + +CCR3 is expressed on basophils and eosinophils, and its use as an exclusion marker +to remove these cells from DC gates — particularly the pDC gate, which relies on +CD123-high expression shared with basophils — is a standard flow cytometry practice. +However, none of the open-access papers fetched for this report contained a verbatim +sentence describing CD193/CCR3 in the context of DC gating or basophil exclusion. +Evidence will be added when a suitable open-access reference is located. + +--- + +## Sources + +| PMID | DOI | Title | Authors | Year | Access | +|------|-----|-------|---------|------|--------| +| 31134067 | 10.3389/fimmu.2019.01088 | Human Dendritic Cell Subsets, Ontogeny, and Impact on HIV Infection | Rhodes JW, Tong O, Harman AN, Turville SG | 2019 | Open access (Frontiers) | +| 28428369 | 10.1126/science.aah4573 | Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors | Villani AC et al. | 2017 | Open access via PMC5775029 | +| 27637149 | 10.1016/j.immuni.2016.08.057 | Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species | Guilliams M, Dutertre CA, Scott CL et al. | 2016 | Open access via PMC5040826 | +| — | 10.1182/blood-2007-04-084210 | Novel markers of normal and neoplastic human plasmacytoid dendritic cells | Garnache-Ottou F et al. | 2008 | Paywalled (ASH Publications HTTP 403) | +| — | 10.1038/s41586-024-07671-y | Plasmacytoid DCs control homeostasis of megakaryopoiesis | Gao Y et al. | 2024 | Paywalled (Nature HTTP 303 auth redirect) | +| — | S1074-7613(20)30321-6 | The More, the Merrier: DC3s Join the Human DC Family | Bosteels C, Scott CL | 2020 | Paywalled (Cell/Immunity HTTP 403) | +| — | 10.1126/science.aah4573 | Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors | Villani AC et al. | 2017 | See PMC row above | +| — | 10.1002/cyto.a.24269 | Comprehensive Phenotyping of Human Dendritic Cells and Monocytes | (Cytometry A) | — | Paywalled (Wiley HTTP 402) | diff --git a/reports/literature/ilc_markers.md b/reports/literature/ilc_markers.md new file mode 100644 index 0000000..fd0d807 --- /dev/null +++ b/reports/literature/ilc_markers.md @@ -0,0 +1,176 @@ +# ILC Marker Literature Support + +Evidence for SOULCAP innate lymphoid cell (ILC) marker definitions, extracted verbatim from open-access papers. +Quotes were extracted via WebFetch from publicly accessible HTML pages; researchers should verify against the primary PDFs. + +**Papers inaccessible (paywalled):** +- Trabanelli et al 2018, Cytometry B (PMID 29244250; DOI 10.1002/cyto.b.21614) — Wiley returned HTTP 402; institutional repositories showed abstract only. +- Vivier et al 2018 "Innate Lymphoid Cells: 10 Years On" Cell (DOI 10.1016/j.cell.2018.09.006) — ScienceDirect returned HTTP 403. +- Serafini et al 2020, Seminars in Cancer Biology (DOI 10.1016/j.semcancer.2020.01.002) — ScienceDirect returned HTTP 403. + +--- + +## Markers with evidence + +### CD127 / IL-7Rα (required positive — pan-ILC marker) + +IL-7 receptor alpha (CD127) is the canonical positive selection marker that defines all helper-ILC subsets and distinguishes them from cytotoxic NK cells. + +> "total ILCs being defined as LIN− CD45+ CD127+" +— Bonne-Année, Bush & Nutman 2019 (PMID:31586075; DOI:10.1038/s41598-019-50308-8) + +> "By first gating on the total ILC population (defined as single cells that were CD45+ Lin-CD127+), these cells could then be divided into their respective ILC subsets" +— Bonne-Année, Bush & Nutman 2019 (PMID:31586075; DOI:10.1038/s41598-019-50308-8) + +> "CD45+Lin–CD3–CD161+CD127+ cells and are subdivided into 3 subsets, namely, group 1 ILCs (ILC1s) (CD117–CRTH2–), group 2 ILCs (ILC2s) (CRTH2+), and group 3 ILCs (ILC3s) (CD117+CRTH2–)." +— Alkon et al 2022 (PMID:34363841; DOI:10.1016/j.jaci.2021.07.025) + +> "characterized by the expression of the pan‐ILC markers CD127, CD161, and CD200R1" +— Krabbendam et al 2021 (PMID:33300130; DOI:10.1002/eji.202048696) + +> "The population positive for CD7, CD45, CD127 and CD161 and negative for LIN2 was separated and divided into CRTH2 positive/NKp46 negative and CRTH2 negative/NKp46 positive." +— Bento et al 2025 (PMID unknown; DOI:10.3389/fimmu.2025.1568875) + +--- + +### CD3 (required exclusion — separates ILC from T cells) + +CD3 negativity is used to exclude T cells before gating on ILC subsets; it is sometimes added to the lineage cocktail and sometimes applied as a standalone gate. + +> "We gated for lymphocytes, excluded doublets and dead cells and selected CD45+CD3− cells" +— Krabbendam et al 2021 (PMID:33300130; DOI:10.1002/eji.202048696) + +> "CD45+Lin–CD3–CD161+CD127+ cells termed ILCs" +— Alkon et al 2022 (PMID:34363841; DOI:10.1016/j.jaci.2021.07.025) + +> "CD3− cells were selected for lineage marker negative (Lin−) status using antibodies against CD3, CD4, TCRαβ, and TCRγδ (T cells), CD19 (B cells) CD14 (monocytes)" +— Krabbendam et al 2021 (PMID:33300130; DOI:10.1002/eji.202048696) + +--- + +### CD161 (NKR-P1; common ILC co-marker) + +CD161 is widely used alongside CD127 to define bona fide ILCs and is described as a pan-ILC marker, though it is not included in the SOULCAP required-positive gate for bulk ILC or the three subsets. + +> "CD45+Lin–CD127+CD161+ cells (ie, bona fide ILCs)" +— Alkon et al 2022 (PMID:34363841; DOI:10.1016/j.jaci.2021.07.025) + +> "Within the Lin−CD127+ population, conventional ILCs expressed CD161 but not CD94" +— Krabbendam et al 2021 (PMID:33300130; DOI:10.1002/eji.202048696) + +> "CD161, which is known to be present on NK cells, NKT cells, and T cells, is also expressed by human ILCs." +— Alkon et al 2022 (PMID:34363841; DOI:10.1016/j.jaci.2021.07.025) + +> "ILC1s were identified through the expression of CD7, CD45, CD127, CD161, absent/low NKp46 and absent LIN2, and CRTH2." +— Bento et al 2025 (PMID unknown; DOI:10.3389/fimmu.2025.1568875) + +**Caveat:** CD161 is shared with NK cells, NKT cells, and some T cells, so it must be combined with CD127 and a Lin-exclusion gate to select ILCs specifically. + +--- + +### CD294 / CRTH2 (required positive on ILC2; required negative on ILC1 and ILC3) + +CRTH2 (prostaglandin D2 receptor 2, encoded by *PTGDR2*) is the defining positive marker for ILC2 and is negative on ILC1 and ILC3. + +> "group 2 ILCs (ILC2s) (CRTH2+), and group 3 ILCs (ILC3s) (CD117+CRTH2–)" +— Alkon et al 2022 (PMID:34363841; DOI:10.1016/j.jaci.2021.07.025) + +> "ILC2s as CRTH2+ CD117−/+" +— Bonne-Année, Bush & Nutman 2019 (PMID:31586075; DOI:10.1038/s41598-019-50308-8) + +> "ILC2 were identified through the positive expression of CD7, CD45, CD127, CD161, CRTH2, absent/low NKp46 and absent LIN2." +— Bento et al 2025 (PMID unknown; DOI:10.3389/fimmu.2025.1568875) + +> "ILC3 were identified through the positive expression of CD7, CD45, CD127, CD161 and NKp46 and absence of CRTH2 and LIN2." +— Bento et al 2025 (PMID unknown; DOI:10.3389/fimmu.2025.1568875) + +> "ILC1s as CD117− CRTH2−" +— Bonne-Année, Bush & Nutman 2019 (PMID:31586075; DOI:10.1038/s41598-019-50308-8) + +--- + +### CD117 / c-Kit (required positive on ILCp and ILC3; required negative on ILC1; low/negative on ILC2) + +CD117 (c-Kit, *KIT*) distinguishes ILC3 (positive) from ILC1 (negative) within the CRTH2-negative compartment, and marks ILC progenitors (ILCp). ILC2 is characteristically CD117 low or negative. + +> "could be subdivided into CD117−NKp44− ILC1s and CD117‐expressing NKp44− ILC3s and NKp44+ ILC3s." +— Krabbendam et al 2021 (PMID:33300130; DOI:10.1002/eji.202048696) + +> "ILC1s as CD117− CRTH2−" … "ILC3s as CRTH2− CD117+" +— Bonne-Année, Bush & Nutman 2019 (PMID:31586075; DOI:10.1038/s41598-019-50308-8) + +> "ILC2s as CRTH2+ CD117−/+" +— Bonne-Année, Bush & Nutman 2019 (PMID:31586075; DOI:10.1038/s41598-019-50308-8) + +> "ILC3 subpopulations were evaluated in whole blood using the NKp44 (44.189) antibody to defined ILC3as as CRTH2− CD117+ NKp44− and ILC3bs as CRTH2− CD117+ NKp44+" +— Bonne-Année, Bush & Nutman 2019 (PMID:31586075; DOI:10.1038/s41598-019-50308-8) + +> "group 3 ILCs (ILC3s) (CD117+CRTH2–)" +— Alkon et al 2022 (PMID:34363841; DOI:10.1016/j.jaci.2021.07.025) + +**Discrepancy flag — Bento et al 2025:** The Frontiers paper (bone marrow / MDS context) states: "Although CD117 (c-KIT) is commonly included in gating strategies to enhance the discrimination among ILC subsets, being highly expressed in ILC progenitors and ILC1, less so in ILC2, and absent in ILC3—we chose not to rely on this marker in our analysis. This decision was based on the context of our study, which involves comparing healthy bone marrow with bone marrow from Myelodysplastic patients, where c-KIT expression may be altered due to potential mutations." The CD117 pattern asserted here (high on ILC1, absent on ILC3) is the reverse of the consensus established by Alkon et al and Bonne-Année et al, and contradicts the SOULCAP definitions. The paper explicitly excluded CD117 from their own gating to avoid c-Kit mutation artefacts in MDS; the bracketed characterisation may contain a transcription error. The standard peripheral-blood consensus (ILC1 CD117−, ILC3 CD117+) should be followed for SOULCAP. + +--- + +### CD56 / NCAM (ILCp required positive; ILC1/ILC2 required negative; ILC3 CD56+/-) + +CD56 is included in lineage-exclusion cocktails in multiple protocols to remove NK cells from the ILC gate. Its optional positive expression on ILC3 subsets is noted separately. + +> "(*) LIN2 is cocktail of the following antibodies: CD3-FITC (SK7), CD14-FITC (SJ25C1), CD19-FITC (L27), CD20-FITC (MφP9), and CD56-FITC (NCAM16.2)." +— Bento et al 2025 (PMID unknown; DOI:10.3389/fimmu.2025.1568875) + +> Lineage markers include: "CD3, CD4, CD8, CD14, CD16, CD19, CD56, CD11c, CD11b, FcεR1a" [Table 2] +— Bonne-Année, Bush & Nutman 2019 (PMID:31586075; DOI:10.1038/s41598-019-50308-8) + +> "Similar to ILC3s, CD94+ ILCs partly expressed NKp44 and IL‐1R1, and also CD117, CD56, NKG2A" +— Krabbendam et al 2021 (PMID:33300130; DOI:10.1002/eji.202048696) + +**Caveat:** CD56 in the lineage gate removes NK cells (CD56+ CD127−). ILC3 can express CD56 at variable levels, which is why SOULCAP encodes ILC3's CD56 as "+/−" rather than requiring it or excluding it. The ILCp gate requires CD56+, which in combination with CD117+ and CD127+ separates it from NK cells (which are CD127−). + +--- + +### Lineage exclusion markers (CD14, CD33, CD64, CD34, CD19, CD15, CD66b, CD123) + +Protocols use a cocktail of lineage antibodies to exclude myeloid cells, B cells, dendritic cells, basophils, and haematopoietic progenitors before gating on ILCs. Specific cocktail composition varies by laboratory. + +> "Subsequently we gated out non‐relevant lineages using antibodies against CD3, CD4, TCRαβ, and TCRγδ (T cells), CD19 (B cells) CD14 (monocytes) FcRεR1a (mast cells), BDCA2 (pDCs), CD123 (pDCs, basophils), and CD34 (hematopoietic progenitors)." +— Krabbendam et al 2021 (PMID:33300130; DOI:10.1002/eji.202048696) + +> "lineage cocktail (TCRα/β, TCRγ/δ, CD19, CD16, CD15, CD14, CD94, CD11c, BDCA-2, FcεRIα, glycophorin A, CD41, CD1a, and CD34)" +— Alkon et al 2022 (PMID:34363841; DOI:10.1016/j.jaci.2021.07.025) + +> "NK cells were excluded by adding anti-CD94 and anti-CD16 antibodies to the lineage cocktail." +— Alkon et al 2022 (PMID:34363841; DOI:10.1016/j.jaci.2021.07.025) + +**Notes on individual markers:** +- **CD14** — present in all four lineage cocktails as a monocyte exclusion marker. +- **CD19** — present in all four lineage cocktails as a B-cell exclusion marker. +- **CD34** — used by Krabbendam et al and Alkon et al to exclude haematopoietic progenitors; consistent with SOULCAP's required exclusion. +- **CD15 / CD66b** — CD15 appears in Alkon et al's cocktail; no paper in this set listed CD66b explicitly (a granulocyte marker that can substitute for CD15). +- **CD123** — listed by Krabbendam et al as covering pDCs and basophils. +- **CD33** — not explicitly named as a lineage marker in any fetched paper; its role as a myeloid exclusion is complementary to CD14. CD64 is also absent from the lineage cocktails documented here, though both are standard additions in more extended panels. + +--- + +## Markers with no direct evidence found + +| Marker | Notes | +|--------|-------| +| CD33 | Not listed in any lineage cocktail in the four fetched papers. Its myeloid-exclusion role is well established in the broader flow cytometry literature but not quoted here. | +| CD64 (FcγRI) | Not listed in any lineage cocktail fetched. CD16 (FcγRIII) is used instead by Alkon et al to exclude NK cells/monocytes. | +| CD66b | Not found in any fetched paper. CD15 covers a similar granulocyte population. | +| ILCp-specific (CD117+CD56+CD294−) | No paper in this set discusses ILCp as a distinct gated population with this exact combination; the ILCp is referenced only in passing by Bonne-Année et al as a possible explanation for circulating CD117+ cells. | + +--- + +## Sources + +| PMID | DOI | Title | Authors | Year | Access | +|------|-----|-------|---------|------|--------| +| 33300130 | 10.1002/eji.202048696 | Identification of human cytotoxic ILC3s | Krabbendam L, Heesters BA, Kradolfer CMA, Spits H, Bernink JH | 2021 | Open access (PMC8248192) | +| 34363841 | 10.1016/j.jaci.2021.07.025 | Single-cell analysis reveals innate lymphoid cell lineage infidelity in atopic dermatitis | Alkon N, Bauer WM, Krausgruber T, et al. | 2022 | Open access (PMC9130781) | +| 31586075 | 10.1038/s41598-019-50308-8 | Differential Modulation of Human Innate Lymphoid Cell (ILC) Subsets by IL-10 and TGF-β | Bonne-Année S, Bush MC, Nutman TB | 2019 | Open access (PMC6778123) | +| PMID unknown | 10.3389/fimmu.2025.1568875 | Innate lymphoid cells in bone marrow and peripheral blood of healthy individuals and in bone marrow of patients with myelodysplastic syndromes | Bento LC, Martelossi Cebinelli G, Bacal NS, Marti LC | 2025 | Open access (Frontiers) | +| 29244250 | 10.1002/cyto.b.21614 | Human innate lymphoid cells (ILCs): Toward a uniform immune-phenotyping | Trabanelli S, Gomez-Cadena A, Salomé B, et al. | 2018 | Paywalled — Wiley HTTP 402; abstract only via institutional repositories | +| unknown | 10.1016/j.cell.2018.09.006 | Innate Lymphoid Cells: 10 Years On | Vivier E, et al. | 2018 | Paywalled — ScienceDirect HTTP 403 | +| unknown | 10.1016/j.semcancer.2020.01.002 | NK cells and ILCs in tumor immunotherapy | Serafini N, et al. | 2020 | Paywalled — ScienceDirect HTTP 403 | diff --git a/reports/literature/inkt_markers.md b/reports/literature/inkt_markers.md new file mode 100644 index 0000000..69e072d --- /dev/null +++ b/reports/literature/inkt_markers.md @@ -0,0 +1,182 @@ +# iNKT Marker Literature Support + +Evidence for SOULCAP invariant NKT (iNKT) cell marker definitions, extracted verbatim from open-access papers. + +This report is also relevant to CL ontology issue #13, which proposes renaming CL:0000814 from "Mature NK T cell" to "iNKT cell". The evidence below supports the view that the SOULCAP iNKT definition corresponds specifically to the invariant (Type I) NKT lineage, which is uniquely defined by the TRAV10/TRAJ18 (TCRVα24-Jα18) invariant α-chain paired with TRBV25-1 (TCRVβ11), and is distinct from Type II NKT (vNKT) cells and from CD56+ T cells more broadly. + +**Paywalled paper (could not be accessed):** Immunol Cell Biol 2020, DOI:10.1111/imcb.12248 — server returned HTTP 402. + +--- + +## Markers with evidence + +### CD3 (required positive — iNKT are T cells) + +iNKT cells are T lymphocytes and therefore express CD3 at the cell surface. The OMIP-046 panel uses CD3 as the principal lineage gate before resolving iNKT cells by their TCR chains. + +> "both identified as CD3+ and defined by their TCR specificities" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +> "we defined iNKT cell subsets by the co-expression of TCR Vα24 and Vβ11 among CD3+ cells, and further through their expression of CD4 and CD161" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +> "gating should include time, singlets, and scatter profile, followed by dead cell exclusion, CD14/CD19 dumping, and CD3 positivity" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +> "the four CD3+ T cell subsets can be gated on, as CD8 and CD4 bulk T cells, MAIT cells, (CD161bright Vα7.2 TCR+), and iNKT cells (Vα24 TCR+ Vβ11 TCR+)" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +--- + +### TCRαβ (required positive; TCRγδ excluded) + +iNKT cells use the αβ T cell receptor. The invariant Vα24-Jα18 and Vβ11 chains are both αβ TCR gene segments, making TCRαβ expression inherent to the iNKT definition. Zhou et al. 2022 explicitly state this as the molecular basis of CD1d recognition. + +> "Expression of T Cell Receptor (TCR)-αβ enables NKT cells to recognize antigenic lipids presented by CD1d" +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +The same paper's gating strategy for Type II NKT (T2NKT) requires TCRγδ exclusion, confirming that NKT cells — including iNKT — are not TCRγδ+ cells: + +> "T2NKT cells were identified as CD3+ CD56+ CD161+ TCR-γδ- TCRVα7.2- and TCRVα24- cells." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +> "we identified a CD3+ CD56+ CD161+ TCR-Vα24- TCR-γδ- TCR-Vα7.2- living T2NKT cell population." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +--- + +### TCRVα24-Jα18 (invariant α-chain — required; identifies iNKT vs vNKT) + +The invariant α-chain (TRAV10/TRAJ18 in IMGT notation; TCRVα24-Jα18 in human, TCRVα14-Jα18 in mouse) is the canonical hallmark of human iNKT cells. Anti-TCRVα24 antibodies are used as a proxy for the full Vα24-Jα18 rearrangement in standard flow cytometry panels; where greater specificity is required the anti-TCRVα24-Jα18 clone 6B11 is used instead. + +> "iNKT cells possess an invariant TCR Vα24-Jα18α chain paired with TCR Vβ11, which mainly responds to α-galactosylceramide glycopeptide (αGalCer)." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +> "iNKT cells, can be identified in humans through expression of their invariant alpha (Vα24) and beta (Vβ11) TCR segments" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +Panel reagent confirmation — Table 2 of OMIP-046 lists the following antibody assignments for iNKT identification: + +> "Vα24 TCR FITC C15 iNKT cell lineage" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +The SOULCAP panel lists "TCRVα24+" as an acceptable proxy for the full TCRVα24-Jα18 rearrangement. The OMIP-046 data directly support this: the Vα24 antibody (clone C15) is used as the iNKT lineage marker in a validated 16-colour human blood panel, consistent with the SOULCAP convention. + +Note on terminology: T2NKT cells are gated as TCRVα24- (Zhou et al. 2022), meaning TCRVα24 positivity is specific to iNKT (Type I) cells within the broader NKT cell category. + +--- + +### TCR Vβ11 / TRBV25-1 (required positive — dominant β-chain in human iNKT) + +TCR Vβ11 (TRBV25-1 in IMGT) is the predominant β-chain partner for the invariant Vα24-Jα18 α-chain in human iNKT cells. It is used in combination with anti-TCRVα24 to gate iNKT cells by flow cytometry. + +> "iNKT cells possess an invariant TCR Vα24-Jα18α chain paired with TCR Vβ11, which mainly responds to α-galactosylceramide glycopeptide (αGalCer)." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +> "iNKT cells, can be identified in humans through expression of their invariant alpha (Vα24) and beta (Vβ11) TCR segments" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +> "we defined iNKT cell subsets by the co-expression of TCR Vα24 and Vβ11 among CD3+ cells, and further through their expression of CD4 and CD161" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +Panel reagent confirmation — Table 2 of OMIP-046: + +> "Vβ11 TCR PE C21 iNKT cell lineage" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +Validation of the Vα24+Vβ11+ co-staining strategy against CD1d pentamer: + +> "the Vα24+Vβ11+ gate encompasses the majority of CD1d pentamer+ cells (median=99%)" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +--- + +### CD1d-α-GalCer Tetramer (alternative iNKT identification) + +CD1d tetramers or pentamers loaded with α-galactosylceramide (α-GalCer) bind the invariant TCR directly, providing an antigen-based alternative to the dual anti-TCRVα24/Vβ11 antibody approach. OMIP-046 validates that these two strategies are essentially equivalent. + +> "the vast majority of α-GalCer loaded CD1d pentamer+ cells fall within the Vα24+Vβ11+ gate (median=99%), and the Vα24+Vβ11+ gate encompasses the majority of CD1d pentamer+ cells (median=99%)" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +> "CD1d and MR1 tetramer can easily be substituted into this panel in place of these MAIT and iNKT TCRs" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +Note on CD1d tetramers and Type II NKT cells: CD1d tetramers loaded with sulfatide (rather than α-GalCer) are used to identify T2NKT cells, but this method is unreliable for broader NKT identification: + +> "Human T2NKT cells are conventionally detected with sulfatide-loaded CD1d tetramers; however, this method is noisy and fails to identify T2NKT cells that recognize other lipids." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +This confirms that α-GalCer-loaded CD1d tetramers/pentamers are specific to iNKT (Type I) cells, while sulfatide-CD1d tetramers target T2NKT — further supporting the SOULCAP use of CD1d-αGalCer tetramer as an iNKT-specific identification reagent. + +--- + +### Distinction: iNKT vs Type II NKT (vNKT) + +This section is directly relevant to CL ontology issue #13 (proposed rename of CL:0000814 from "Mature NK T cell" to "iNKT cell"). The literature clearly divides NKT cells into two distinct lineages by TCR specificity. The SOULCAP iNKT definition applies only to Type I (invariant) NKT cells. + +> "NKT cells are subclassified into invariant NKT (iNKT) cells and type II NKT (T2NKT) cells according to their TCR specificity." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +> "iNKT cells possess an invariant TCR Vα24-Jα18α chain paired with TCR Vβ11, which mainly responds to α-galactosylceramide glycopeptide (αGalCer)." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +> "By contrast, T2NKT cells utilize different TCR rearrangements to recognize diverse lipids." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +> "NKT cells are non-conventional T cells that share common features with NK cells." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +The gating strategy for T2NKT explicitly excludes Vα24+ cells, confirming that the two populations are non-overlapping: + +> "T2NKT cells were identified as CD3+ CD56+ CD161+ TCR-γδ- TCRVα7.2- and TCRVα24- cells." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +Implication for CL:0000814: The current CL term name "Mature NK T cell" does not distinguish between Type I (iNKT) and Type II (T2NKT). The SOULCAP definition — which requires TCRVα24-Jα18 (or TCRVα24 proxy, or CD1d-αGalCer tetramer) and TCRVβ11 — corresponds exclusively to the iNKT (Type I) lineage. The proposed rename to "iNKT cell" would therefore accurately reflect the SOULCAP cell type. + +--- + +### Distinction: iNKT vs CD56+ T cells + +iNKT cells may co-express CD56 (which is used as a positive marker for T2NKT identification in Zhou et al. 2022), but CD56 expression alone does not define the NKT lineage. T2NKT cells are gated as CD3+CD56+ before TCR marker exclusions are applied, demonstrating that many CD3+CD56+ T cells are not NKT cells: + +> "T2NKT cells were identified as CD3+ CD56+ CD161+ TCR-γδ- TCRVα7.2- and TCRVα24- cells." +— Zhou et al. 2022 (PMID:35720369; DOI:10.3389/fimmu.2022.898473) + +No verbatim statement distinguishing iNKT from non-NKT CD56+ T cells was found in the fetched papers. The SOULCAP iNKT definition does not include CD56 as a required positive or exclusion, relying instead on TCRVα24-Jα18 / TCRVβ11 or CD1d-αGalCer tetramer to establish iNKT identity. + +--- + +### CD14 / CD19 (lineage exclusion markers) + +The OMIP-046 gating strategy uses CD14 and CD19 as a dump channel to exclude monocytes and B cells before resolving CD3+ T cell subsets (including iNKT). + +> "gating should include time, singlets, and scatter profile, followed by dead cell exclusion, CD14/CD19 dumping, and CD3 positivity" +— Lal et al. 2018 (PMID:29533501; DOI:10.1002/cyto.a.23357) + +--- + +### CD20 / CD33 / CD64 / CD123 / CD16 (exclusion markers) + +No verbatim text was found in the fetched open-access papers explicitly addressing these exclusion markers in the context of iNKT identification. They are routinely used in multi-lineage dump channels for flow cytometry panels (CD20 = B cells; CD33/CD64 = myeloid; CD123 = plasmacytoid dendritic cells/basophils; CD16 = NK cells and granulocytes) but none of the two accessible papers enumerated all of them for the iNKT gate. The OMIP-046 paper mentions CD14/CD19 dumping; no additional exclusion markers are described in that panel for iNKT specifically. + +--- + +## Markers with no direct evidence found + +- **CD20** — not mentioned in fetched papers in the context of iNKT gating. +- **CD33 / CD64** — not mentioned in fetched papers in the context of iNKT gating. +- **CD123** — not mentioned in fetched papers in the context of iNKT gating. +- **CD16** — not mentioned in fetched papers in the context of iNKT gating (ideal exclusion per SOULCAP). +- **HLA-DR / CD11c** — not mentioned in fetched papers. +- **CD15 / CD66b** — not mentioned in fetched papers. +- **TCRγδ (explicit iNKT exclusion)** — no paper stated verbatim that iNKT cells are TCRγδ-; however, the exclusive use of αβ TCR gene segments (Vα24-Jα18 / Vβ11) makes TCRγδ expression biochemically impossible, and the T2NKT gating in Zhou et al. 2022 requires TCRγδ- as a dump marker for all NKT types. + +--- + +## Sources + +| PMID | DOI | Title | Authors | Year | Access | +|------|-----|-------|---------|------|--------| +| 29533501 | 10.1002/cyto.a.23357 | OMIP-046: Characterization of invariant T cell subset activation in humans | Lal KG, Leeansyah E, Sandberg JK, Eller MA | 2018 | Open access (PMC6059363) | +| 35720369 | 10.3389/fimmu.2022.898473 | Identification and Isolation of Type II NKT Cell Subsets in Human Blood and Liver | Zhou JY, Werner JM, Glehr G, Geissler EK, Hutchinson JA, Kronenberg K | 2022 | Open access (Frontiers in Immunology) | +| — | 10.1111/imcb.12248 | The peripheral differentiation of human natural killer T cells | — | 2020 | **Paywalled (HTTP 402)** | diff --git a/reports/literature/t_cell_markers.md b/reports/literature/t_cell_markers.md new file mode 100644 index 0000000..6323bc9 --- /dev/null +++ b/reports/literature/t_cell_markers.md @@ -0,0 +1,369 @@ +# T Cell Marker Literature Support + +Evidence for SOULCAP T cell and T helper subset marker definitions, extracted verbatim from open-access papers. +Paywalled papers are noted where applicable; no text was fabricated from them. + +> **Extraction note.** Quotes below were obtained via the WebFetch web-content extraction tool, +> which uses an AI model to copy text from the fetched page. Where the extracted text is not a +> clean sentence (e.g. gating strings reproduced from a table), the quote is presented exactly as +> returned and the likely source (table, figure legend, methods) is noted. Any suspected OCR/ +> extraction artefacts are flagged inline. + +--- + +## Markers with evidence + +### CD3 (required positive — pan-T cell marker) + +**Context.** CD3 is the invariant signalling component of the T cell receptor complex, expressed +on all mature T cells. It is used as the primary gating marker to gate the T cell compartment +from total PBMCs. + +The HIPC standardisation study (Finak et al. 2016) built a T-cell panel with CD3 as the primary +gate and defined all T cell subsets as CD3+: + +> "CD3+/CD8−/CD4+/CCR7+/CD45RA+" \[CD4 Naïve — Table 2 gating string\] + +> "CD3+/CD8+/CD4−/CCR7+/CD45RA+" \[CD8 Naïve — Table 2 gating string\] + +— Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) + +The blinatumomab/αβγδ study (Kelm et al. 2026) confirmed CD3 as the entry gate for all +T cell subpopulations: + +> "Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell +> populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR +> monoclonal antibodies." + +— Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) + +--- + +### CD4 and CD8 (lineage markers for T helper and cytotoxic T cells) + +The HIPC paper defines CD4 and CD8 as orthogonal lineage markers within the CD3+ gate: + +> "CD3+/CD8−/CD4+/CCR7+/CD45RA−" \[CD4 Central Memory — Table 2 gating string\] + +> "CD3+/CD8+/CD4−/CCR7+/CD45RA+" \[CD8 Naïve — Table 2 gating string\] + +— Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) + +The systemic-sclerosis/Th2 study (Zhu et al. 2026) also uses CD4 as the entry requirement +for T helper subset analysis: + +> "cluster 9 was defined as Th2 cells, as they highly expressed CCR4 but did not express +> biomarkers of Tfh cells (CXCR5, PD-1), Th1 cells (CXCR3), Th17 cells (CCR6), and Treg +> cells (CD25, Foxp3)" + +— Zhu H et al. 2026 (PMID: 41826820; DOI: 10.1186/s10020-026-01455-y; PMC: PMC13101149) + +--- + +### TCRαβ vs TCRγδ (distinguishing αβ from γδ T cells) + +> "Purity of PHA- and Zole- expanded αβ and γδ T-cell cultures and MACS-isolated T-cell +> populations were assessed by flow cytometry using anti-CD3, CD4, CD8, γδ TCR, and αβ TCR +> monoclonal antibodies." + +— Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) + +*Interpretation.* Anti-αβ TCR and anti-γδ TCR antibodies are used together with CD3 to +distinguish the two major TCR lineages; CD4 and CD8 further resolve subsets within the αβ +compartment. The Vδ2 γδ subset in the same paper is described using memory markers (see +CD27/CD28 section below). + +--- + +### CD183 / CXCR3 (Th1 marker — positive on Th1, negative on Th2/Th17) + +Multiple independent studies converge on CXCR3 (CD183) as a positive marker of Th1 +and a negative marker that excludes Th2: + +> "Th1, CXCR3+CCR6–; Th17, CXCR3–CCR6+; Th1–17, CXCR3+CCR6+" \[Figure 1 description\] + +> "Th1 (CXCR3+CCR6–CCR4–), Th2 (CXCR3–CCR6–CCR4+), Th17 (CXCR3–CCR6+CCR4+)" +> \[Figure 3 description\] + +— Nalubega M et al. 2026 (PMID: 41757944; DOI: 10.1093/infdis/jiag115; PMC: PMC13127770) + +> "Th1 (CXCR3+CCR4−CCR6− CD62LlowCD4+ T cells)" + +— Kamigaichi A et al. 2026 (PMID: 42047825; DOI: 10.1007/s00262-026-04357-4; PMC: PMC13125411) + +> "define (C) CD154+ Th1 (CXCR3+CCR4−CCR10−CCR6−), (D) CD154+ Th2 +> (CXCR3−CCR4+CCR10−CCR6−), (E) CD154+ Th17 (CXCR3−CCR4+CCR10−CCR6+)" + +— Pospich R et al. 2026 (PMID: 42327791; DOI: 10.3389/fimmu.2026.1798583; PMC: PMC13275367) + +> "Th1 (CXCR3+ CCR6−), Th17 (CXCR3− CCR6+), and Th2 (CXCR3− CCR6−" \[figure legend; +> Th2 further defined as CCR4+\] + +— Gholizadeh F et al. 2026 (PMID: 41928597; DOI: 10.1002/eji.70177; PMC: PMC13047356) + +The Th9-differentiation review (Frontiers Immunology 2020) also lists CXCR3 on Th9 cells, +reinforcing its cross-subset utility: + +> "human Th9 cells express CD183 (CXCR3), CD193 (CCR3), and CD196 (CCR6), but not +> CD194+(CCR4+) or D294 (CRTH2), which are expressed on the surface of Th2 cells" + +*Note: "D294" is a likely extraction artefact for "CD294" (CRTH2).* + +— Frontiers Immunology 2020 (DOI: 10.3389/fimmu.2020.01026) + +--- + +### CD185 / CXCR5 (Tfh marker — positive on follicular helper T cells) + +Three independent studies identify circulating Tfh (pTfh) cells by CXCR5 positivity within the +CD4+ gate: + +> "CXCR5+ Tfh vs. CXCR5− non‐Tfh" \[figure description\] + +— Gholizadeh F et al. 2026 (PMID: 41928597; DOI: 10.1002/eji.70177; PMC: PMC13047356) + +> "CD3+CD4+CD45RO+PD-1highCXCR5+" \[circulating Tfh cell definition\] + +> "CD3+CD4+CD45RO+PD-1highCXCR5−" \[circulating peripheral helper T cell definition\] + +— Liao H et al. 2025 (PMID: 41351179; DOI: 10.1186/s13075-025-03701-w; PMC: PMC12797565) + +> "pTfh (CXCR5+PD1+)" \[Methods section\] + +> "pTfh1 (CXCR3+CCR6–), pTfh2 (CXCR3–CCR6–), pTfh17 (CXCR3–CCR6+)" \[Methods section\] + +— Nalubega M et al. 2026 (PMID: 41757944; DOI: 10.1093/infdis/jiag115; PMC: PMC13127770) + +The sarcoidosis/COVID study also lists CXCR5 as one of four chemokine receptor antibodies used +to identify polarised Th subsets: + +> "we used the following anti-chemokine receptors antibodies – CXCR5, CCR6, CXCR3, and CCR4" + +— Starshinova A et al. 2025 (PMID: 41376646; DOI: 10.3389/fimmu.2025.1614461; PMC: PMC12685880) + +--- + +### CD194 / CCR4 (Th2 and Th17 marker — positive on Th2, variable on Th17) + +CCR4 (CD194) is consistently positive on Th2 cells; it is also positive on Th17 (but combined +with CCR6) in several gating schemes: + +> "Th2 (CXCR3–CCR6–CCR4+), Th17 (CXCR3–CCR6+CCR4+)" \[Figure 3 description\] + +— Nalubega M et al. 2026 (PMID: 41757944; DOI: 10.1093/infdis/jiag115; PMC: PMC13127770) + +> "cluster 9 was defined as Th2 cells, as they highly expressed CCR4 but did not express +> biomarkers of Tfh cells (CXCR5, PD-1), Th1 cells (CXCR3), Th17 cells (CCR6), and Treg +> cells (CD25, Foxp3)" + +— Zhu H et al. 2026 (PMID: 41826820; DOI: 10.1186/s10020-026-01455-y; PMC: PMC13101149) + +> "Th2 (CXCR3−CCR4+CCR6− CD62LlowCD4+ T cells)" + +> "Th17 (CXCR3−CCR4+CCR6+ CD62LlowCD4+ T cells)" + +— Kamigaichi A et al. 2026 (PMID: 42047825; DOI: 10.1007/s00262-026-04357-4; PMC: PMC13125411) + +> "We detected predominantly the marker combination described for Th2 cells +> (Figure 2D, CXCR3−CCR6−CCR10−CCR4+) and Th17 cells +> (Figure 2E, CXCR3−CCR6+CCR4+CCR10−) on SplB-specific T cells." + +— Pospich R et al. 2026 (PMID: 42327791; DOI: 10.3389/fimmu.2026.1798583; PMC: PMC13275367) + +> "human Th9 cells express CD183 (CXCR3), CD193 (CCR3), and CD196 (CCR6), but not +> CD194+(CCR4+) or D294 (CRTH2), which are expressed on the surface of Th2 cells" + +*Note: Th9 cells are CCR4-negative, further supporting CCR4 as a Th2/Th17 marker not a Th1/Th9 marker.* + +— Frontiers Immunology 2020 (DOI: 10.3389/fimmu.2020.01026) + +--- + +### CD196 / CCR6 (Th17 marker — positive on Th17, negative on Th1/Th2) + +> "Th17 (CXCR3–CCR6+CCR4+)" \[Figure 3\] + +> "pTfh17 (CXCR3–CCR6+)" \[Methods\] + +— Nalubega M et al. 2026 (PMID: 41757944; DOI: 10.1093/infdis/jiag115; PMC: PMC13127770) + +> "CD154+ Th17 (CXCR3−CCR4+CCR10−CCR6+)" + +— Pospich R et al. 2026 (PMID: 42327791; DOI: 10.3389/fimmu.2026.1798583; PMC: PMC13275367) + +> "Th17 (CXCR3−CCR4+CCR6+ CD62LlowCD4+ T cells)" + +— Kamigaichi A et al. 2026 (PMID: 42047825; DOI: 10.1007/s00262-026-04357-4; PMC: PMC13125411) + +> "human Th9 cells express CD183 (CXCR3), CD193 (CCR3), and CD196 (CCR6)" + +*Note: CD196 is used here as the CD number synonym for CCR6, and Th9 cells are CCR6+ in this +study, making CCR6+ insufficient alone to define Th17; the full combination with CXCR3- and +CCR4+/- is required.* + +— Frontiers Immunology 2020 (DOI: 10.3389/fimmu.2020.01026) + +The memory Th subset nicotine paper confirms the key three-way partition using only CXCR3 and +CCR6 as two axes: + +> "Th1 (CXCR3+ CCR6−), Th17 (CXCR3− CCR6+), and Th2 (CXCR3− CCR6−" + +— Gholizadeh F et al. 2026 (PMID: 41928597; DOI: 10.1002/eji.70177; PMC: PMC13047356) + +--- + +### CD294 / CRTH2 (Th2 marker — helps distinguish Th2 from Th9) + +Direct evidence for CD294/CRTH2 as a Th2 surface marker comes from the Th9 review, which +lists CRTH2 as expressed on Th2 but absent on Th9: + +> "human Th9 cells express CD183 (CXCR3), CD193 (CCR3), and CD196 (CCR6), but not +> CD194+(CCR4+) or D294 (CRTH2), which are expressed on the surface of Th2 cells" + +*"D294" is a likely OCR/extraction artefact; the text intends "CD294 (CRTH2)".* + +— Frontiers Immunology 2020 (DOI: 10.3389/fimmu.2020.01026) + +*Note.* No additional open-access paper in the current fetch set provided a standalone verbatim +sentence confirming CRTH2 expression on Th2 cells. The OMIP-017 paper (Cytometry A 2012; +DOI: 10.1002/cyto.a.22269) and the Nature Reviews Immunology 2025 guidelines paper were both +paywalled. The Th9 review quote above is the primary open-access verbatim source. + +--- + +### CD25 and CD127lo/- (Treg markers — CD25+CD127low defines regulatory T cells) + +Two independent open-access papers provide verbatim support for the CD25-high, CD127-low +definition of Tregs: + +> "Tregs are typically identified by the expression of the transcription factor FoxP3 or the +> IL-2 receptor α-chain (CD25)...the absence or low expression of the IL-7 receptor α-chain +> (CD127) has been proposed as a distinguishing marker for Tregs" + +> "In humans, a combination of high CD25 and low or absent CD127 expression helps differentiate +> Tregs from effector T cells, which usually express high levels of CD127" + +— Kamran M et al. 2025 (PMID: 41394832; DOI: 10.3389/fimmu.2025.1676937; PMC: PMC12695756) + +> "Expression of CD127, the α-chain of the IL‐7 receptor, is inversely correlated with the +> expression of hallmark Treg cell regulator FOXP3." + +> "the CD4+CD25+CD127low/– population arguably contains a mixture of Treg cells with variable +> degrees of commitment to the Treg cell lineage." + +— Morgana F et al. 2026 (PMID: 41645582; DOI: 10.1002/eji.70107; PMC: PMC12877429) + +The malaria study confirms the same CD25 marker in a gating panel context: + +> "Tregs (FOXP3+CD25+), pTfh (CXCR5+PD1+)" \[Results section\] + +> "nonnaive CD4 T cells" analyzed using "FOXP3, CD45RA, CD25, CCR4, CCR6, CXCR5, CXCR3, +> and CD127" \[Methods\] + +— Nalubega M et al. 2026 (PMID: 41757944; DOI: 10.1093/infdis/jiag115; PMC: PMC13127770) + +--- + +### CD161 (Th17 and MAIT cell marker) + +No verbatim sentence about CD161 as a T helper or MAIT gate marker was found in the +open-access papers fetched in this study. CD161 evidence is absent from all 12 papers accessed. +See the "Markers with no direct evidence" section below. + +--- + +### CD45RA and CCR7 (T cell memory markers) + +**Context.** CD45RA and CCR7 together define four canonical maturation subsets: naïve +(CD45RA+CCR7+), central memory (CD45RA−CCR7+), effector memory (CD45RA−CCR7−), and +TEMRA (CD45RA+CCR7−). + +The HIPC standardisation study provides gating strings for these subsets directly: + +> "CD3+/CD8−/CD4+/CCR7+/CD45RA+" \[CD4 Naïve — Table 2\] + +> "CD3+/CD8−/CD4+/CCR7+/CD45RA−" \[CD4 Central Memory — Table 2\] + +> "CD3+/CD8−/CD4+/CCR7−/CD45RA+" \[CD4 Effector — Table 2\] + +— Finak G et al. 2016 (PMID: 26861911; DOI: 10.1038/srep20686; PMC: PMC4748244) + +The sarcoidosis study applies CD45RA and CCR7 to produce the classic four-subset partition: + +> "CD45RA and CCR7 – CD4+ T cells were divided into four maturation subsets" + +— Starshinova A et al. 2025 (PMID: 41376646; DOI: 10.3389/fimmu.2025.1614461; PMC: PMC12685880) + +The memory Th subset study names specific populations using CCR7: + +> "CD4+ CD45RA− CCR7+ cells for Tcm and CD3+ CD4+ CD45RO+ CCR7− cells for Tem" + +— Gholizadeh F et al. 2026 (PMID: 41928597; DOI: 10.1002/eji.70177; PMC: PMC13047356) + +--- + +### CD27 and CD28 (additional memory/effector T cell markers) + +> "For all analyses, cells were gated on singlets and live cells defined based on scatter +> properties, followed by CD3+ lymphocytes and subsequent αβ/γδ and memory−subset gates" +> with markers including "CD27, CD28, CD45RA, CCR7" used to distinguish naïve, central +> memory (CM), and effector memory (EM) subsets. + +> "Zole-expanded Vδ2 γδ T cells displayed a highly homogeneous effector memory (EM) phenotype +> (CD27−CD45RA−)" + +— Kelm M et al. 2026 (PMID: 41727470; DOI: 10.3389/fimmu.2026.1739493; PMC: PMC12920462) + +*Note.* The SOULCAP EM3 subset (CD45RA−CCR7−CD27−CD28−) adds CD28 negativity as an extra +discriminant beyond standard EM. The Scandinavian Journal of Immunology 2022 COVID paper +(DOI: 10.1111/sji.13217) that originally described EM3 was **paywalled** (HTTP 402) and could +not be accessed. Kelm et al. 2026 confirms CD27, CD28, CD45RA and CCR7 are routinely used +together as the memory panel for both αβ and γδ T cell subsets. + +--- + +### CD14 / CD19 / CD20 / CD123 (exclusion markers for the T cell gate) + +No verbatim sentence describing CD14, CD19, CD20, or CD123 as T cell exclusion markers was +found in the open-access papers accessed in this study. These markers are standard for the +"dump channel" or live-cell/lineage exclusion in multicolour T cell panels but the papers +fetched do not explicitly name them in the gating text that was captured. + +--- + +## Markers with no direct evidence found + +| Marker | Reason for gap | +|--------|---------------| +| **CD161** | Absent from all 12 papers fetched. CD161 is a key marker to identify IL-17-producing cells and MAIT cells but it did not appear in the text segments extracted. A dedicated MAIT/Th17 paper (e.g. Cosmi et al. 2008 JEM; Muñoz-Calleja et al.) would provide this. | +| **CD14 / CD19 / CD20 / CD123 (exclusions)** | No open-access paper in the fetched set included a verbatim sentence naming these as dump-channel markers for T cell gates. Standard practice is to include anti-CD14, anti-CD19, anti-CD20 (B cells, monocytes) and anti-CD123 (plasmacytoid DCs and basophils) in a dump gate but this was not captured verbatim. | +| **CD294 / CRTH2 standalone** | Only one open-access sentence found, in the Th9 review, and it contains a probable extraction artefact ("D294"). OMIP-017 (paywalled) would be the canonical source. | + +--- + +## Paywalled papers (could not access) + +| Paper | URL | HTTP status | Notes | +|-------|-----|-------------|-------| +| Effector memory EM3 COVID paper (Scandinavian J Immunol 2022) | https://onlinelibrary.wiley.com/doi/10.1111/sji.13217 | 402 Payment Required | Key paper for CD45RA−CCR7−CD27−CD28− EM3 subset | +| OMIP-017: T helper subsets (Cytometry A 2012) | https://onlinelibrary.wiley.com/doi/pdf/10.1002/cyto.a.22269 | 402 Payment Required | Canonical CXCR3/CXCR5/CCR4/CCR6 T helper panel | +| Guidelines for T cell nomenclature (Nature Rev Immunol 2025) | https://www.nature.com/articles/s41577-025-01238-2 | 303 → auth wall | Key consensus document for T cell subset definitions | + +--- + +## Sources + +| PMID | DOI | Title (abbreviated) | Authors | Year | Access | +|------|-----|---------------------|---------|------|--------| +| 26861911 | 10.1038/srep20686 | Standardizing Flow Cytometry Immunophenotyping Analysis from the HIPC | Finak G et al. | 2016 | Open (PMC4748244) | +| — | 10.3389/fimmu.2020.01026 | Th9 Cell Differentiation and Its Dual Effects in Tumor Development | (Frontiers Immunol) | 2020 | Open | +| 41928597 | 10.1002/eji.70177 | Nicotine Suppresses Human Memory Th Cell Subsets … α7 nAChR | Gholizadeh F et al. | 2026 | Open (PMC13047356) | +| 41351179 | 10.1186/s13075-025-03701-w | Circulating peripheral helper T cells in granulomatosis with polyangiitis | Liao H et al. | 2025 | Open (PMC12797565) | +| 41757944 | 10.1093/infdis/jiag115 | Comparison of CD4 T-Cell Response in P. falciparum and vivax Malaria | Nalubega M et al. | 2026 | Open (PMC13127770) | +| 41826820 | 10.1186/s10020-026-01455-y | ICOS+ T helper 2 cells promote pulmonary fibrosis in systemic sclerosis | Zhu H et al. | 2026 | Open (PMC13101149) | +| 42327791 | 10.3389/fimmu.2026.1798583 | S. aureus SplB elicits type 1/type 2 response in atopic dermatitis | Pospich R et al. | 2026 | Open (PMC13275367) | +| 41376646 | 10.3389/fimmu.2025.1614461 | Immune responses in pulmonary sarcoidosis following COVID-19 | Starshinova A et al. | 2025 | Open (PMC12685880) | +| 42047825 | 10.1007/s00262-026-04357-4 | Immunological impact of lymph node dissection on Th1-like CD4+ T cells in lung cancer | Kamigaichi A et al. | 2026 | Open (PMC13125411) | +| 41394832 | 10.3389/fimmu.2025.1676937 | CD4 T cell dynamics in visceral leishmaniasis — Tregs | Kamran M et al. | 2025 | Open (PMC12695756) | +| 41645582 | 10.1002/eji.70107 | Isolation of Pure Stable Human Treg Cells Based on GPA33 Expression | Morgana F et al. | 2026 | Open (PMC12877429) | +| 41727470 | 10.3389/fimmu.2026.1739493 | Blinatumomab-driven T-cell activation in αβ and γδ T-cell subsets | Kelm M et al. | 2026 | Open (PMC12920462) | From fcd39516d75964390db2621422432afbdc98e0d9 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Sat, 18 Jul 2026 20:08:09 -0400 Subject: [PATCH 5/8] =?UTF-8?q?feat:=20Milestone=202=20=E2=80=94=20B=20cel?= =?UTF-8?q?l=20and=20gdT+MAIT=20marker=20literature=20reports?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-Authored-By: Claude Sonnet 4.6 --- reports/literature/b_cell_markers.md | 339 +++++++++++++++++++++++++ reports/literature/gdt_mait_markers.md | 209 +++++++++++++++ 2 files changed, 548 insertions(+) create mode 100644 reports/literature/b_cell_markers.md create mode 100644 reports/literature/gdt_mait_markers.md diff --git a/reports/literature/b_cell_markers.md b/reports/literature/b_cell_markers.md new file mode 100644 index 0000000..7d8d087 --- /dev/null +++ b/reports/literature/b_cell_markers.md @@ -0,0 +1,339 @@ +# B Cell Marker Literature Support + +Evidence for SOULCAP B cell marker definitions, extracted verbatim from open-access papers. +Papers marked [PAYWALLED] were inaccessible: the Nature Immunology 2021 review +(PMID 34725481), the Blood 2020 comprehensive analysis (DOI 10.1182/blood.2019002782), +and the Clinical and Experimental Immunology 2021 DN B cell paper (PMID 34075582) +all returned gated or payment-required responses. Verbatim quotes below come from +five fully open-access sources. + +--- + +## Markers with evidence + +### CD19 and CD20 (required positive — pan-B cell markers) + +Context: CD19 is expressed on all B-lineage cells from pro-B to memory stage; CD20 is +expressed from pre-B to memory but is lost as cells commit to the antibody-secreting +(plasmablast/plasma cell) fate. Either marker can gate the B cell compartment, but CD19 +is more stable across differentiation and therefore preferred when including ASCs. + +> "Mature B cells typically express both CD19 and CD20." +— Griffin & Rothstein 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) + +> "as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 +> remains, as CD38/CD138 is acquired" +— Griffin & Rothstein 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) + +> "CD19+ B cells were then enriched to >98% using CD19 microbead magnetic separation" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) + +> "to positively select intact cells (Ir191+Ir193+), to positively select live cells +> (Rh103−Ir191+Ir193+), and to identify CD19+ and/or CD20+ B cells" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) +[mass cytometry (CyTOF) gating strategy; Ir/Rh channels are isotope labels, not surface markers] + +--- + +### CD27 (memory vs naive distinguisher — positive on memory B cells) + +Context: CD27, a TNF receptor superfamily member, is the canonical human memory B cell +marker. Naive and transitional B cells are CD27−; classical memory B cells are CD27+. +Double-negative (DN) B cells are IgD−CD27−, lacking both the naive marker IgD and the +memory marker CD27. + +> "transitional (IgD+CD27−CD10+), and naïve (IgD+CD27−CD10−)" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) + +> "**M**: CD19+ CD27+ CD38−/lo" [memory B cell gating entry] and +> "**N**: CD19+ CD27− CD38− CD24− IgD+" [naive B cell gating entry, Table 1] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "Double negative (DN) B cells, also known as atypical memory B cells, constitute a B cell +> population that lacks expression of immunoglobulin D and CD27 memory marker." +— Sachinidis & Garyfallos 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) + +--- + +### CD38 (differentiation marker — high on transitional B cells and antibody-secreting cells) + +Context: CD38 expression is graded across B cell differentiation: highest on T1 transitional +cells and antibody-secreting cells (ASCs, including plasmablasts and plasma cells); +intermediate on later transitional subsets; low-to-negative on mature naive and memory B cells. +This gradient makes CD38 a key axis in B cell panel design. + +> "T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and +> T3 (CD38+CD24+IgD+ABCB1−)" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) + +> "Co-expression of high levels of CD24 and CD38 have also frequently been used to identify +> them, and it is important that CD27 be included if this is the case" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) +[refers to transitional B cells] + +> "**ASC**: CD19+ CD27+ CD38hi" and "**M**: CD19+ CD27+ CD38−/lo" and +> "**Tr**: CD19+ CD27− CD38int CD24+" [gating table entries, Table 1] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +--- + +### CD10 (transitional B cell marker — high on T1/T2; low on T3; negative on mature) + +Context: CD10 (CALLA, common acute lymphoblastic leukemia antigen) marks immature and +transitional B cells in the periphery and is downregulated as cells reach the mature naive +stage. The T1 subset has the highest CD10 expression; T3 is CD10−; mature naive B cells +are CD10−. + +> "These cells express IgD and CD10 alongside the IgM BCR so can be identified as +> IgD+ CD27−CD10hi/+" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) + +> "T1 (CD38+++CD24hiCD10++IgDlo/−), T2 (CD38++CD24hiCD10+IgD+), and +> T3 (CD38+CD24+IgD+ABCB1−)" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) + +> "transitional (IgD+CD27−CD10+), and naïve (IgD+CD27−CD10−)" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) + +> "CD21lo Tr cells expressed higher levels of markers of the early transitional compartment +> (IgM, CD24, CD10), but less CD21 and CXCR5" +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +--- + +### CD24 (differentiation marker — high on transitional; low on naive; negative on DN B cells) + +Context: CD24 (heat-stable antigen, HSA) is co-expressed with CD38 at high levels on +transitional B cells. Its expression decreases as cells mature to naive stage and is absent +on double-negative B cells. CD24 alongside CD38 is used to resolve the transitional B cell +compartment, and CD24 negativity helps distinguish naive and DN B cells. + +> "Co-expression of high levels of CD24 and CD38 have also frequently been used to identify +> them, and it is important that CD27 be included if this is the case" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) +[refers to transitional B cells] + +> "**Tr**: CD19+ CD27− CD38int CD24+" [transitional B cell gating entry, Table 1] and +> "**N**: CD19+ CD27− CD38− CD24− IgD+" [naive B cell gating entry] and +> "**DN**: CD19+ CD27− CD38− CD24− IgD−" [double-negative B cell gating entry] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +--- + +### IgD (class-switch indicator — positive on naive; negative on class-switched memory) + +Context: IgD is co-expressed with IgM on the surface of naive and some transitional B cells. +It is lost during class-switch recombination. Unswitched memory B cells (SOULCAP: +Unswitched, IgM-only) retain IgD or IgM surface expression; switched memory cells lose +both. IgD negativity is also the defining criterion of double-negative B cells. + +> "naïve B cells express immunoglobulin (Ig)D and IgM and undergo isotype switching to +> produce IgM, IgA, IgG, or IgE exclusively" +— McGrath, Li & Wilson 2022 (PMID: 35393268; DOI: 10.1016/j.it.2022.03.005) + +> "**N**: CD19+ CD27− CD38− CD24− IgD+" [naive B cell gating entry, Table 1] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "**usM**: IgM+ IgD+" [unswitched memory] / "**mM**: IgM+ IgD−" [IgM-only memory] / +> "**sM**: IgM− IgD−" [switched memory] [gating table entries, Table 1] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "Double negative (DN) B cells, also known as atypical memory B cells, constitute a B cell +> population that lacks expression of immunoglobulin D and CD27 memory marker." +— Sachinidis & Garyfallos 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) + +> "T2 (CD38++CD24hiCD10+IgD+), and T3 (CD38+CD24+IgD+ABCB1−)" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) +[IgD present on T2 and T3 transitional cells; absent or low on T1] + +--- + +### IgM, IgG, IgA, IgE (class-switch subtype markers on switched memory B cells) + +Context: After class-switch recombination, memory B cells express exactly one antibody heavy +chain isotype. Unswitched memory cells co-express IgM with IgD; IgM-only memory cells +express IgM without IgD; class-switched memory cells have lost both IgM and IgD in favour +of IgG, IgA, or IgE. The SOULCAP IgA, IgG, and IgE subtypes subdivide the switched +memory (IgD−IgM−) gate by the newly acquired isotype. + +> "naïve B cells express immunoglobulin (Ig)D and IgM and undergo isotype switching to +> produce IgM, IgA, IgG, or IgE exclusively" +— McGrath, Li & Wilson 2022 (PMID: 35393268; DOI: 10.1016/j.it.2022.03.005) + +> "CD73+ MBCs are also proportionally more isotype-switched than CD73– MBCs, allowing them +> to produce IgG and IgA antibodies to facilitate a more diverse set of effector functions" +— McGrath, Li & Wilson 2022 (PMID: 35393268; DOI: 10.1016/j.it.2022.03.005) + +> "cluster 4 was IgG1 (IGHG1) dominant with minimal contributions from other isotypes, +> cluster 7 was more balanced but with a slight bias towards IgA (IGHA1/IGHA2) overall" +— McGrath, Li & Wilson 2022 (PMID: 35393268; DOI: 10.1016/j.it.2022.03.005) +[single-cell transcriptomics of memory B cell clusters] + +> "**usM**: IgM+ IgD+" [unswitched memory] / "**mM**: IgM+ IgD−" [IgM-only memory] / +> "**sM**: IgM− IgD−" [switched memory, IgG/IgA/IgE positive by exclusion] [Table 1] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "Consistent with the B cell antigen receptor-sequencing data, SARS-CoV-2-specific +> responsiveness was broad, with participation of IgM, IgA and IgG antibodies." +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +--- + +### CD138 / Syndecan-1 (plasma cell marker — distinguishes PC from PB) + +Context: CD138 (Syndecan-1, SDC1) is a heparan-sulphate proteoglycan upregulated as +plasmablasts (CD138−CD38hi) mature into plasma cells (CD138+CD38hi). Within the +SOULCAP panel the CD138 axis separates PC (CD138+) from PB (CD138−) within the +CD19+CD27+/hiCD38hi gate. CD20 is simultaneously lost at the plasmablast stage. + +> "as B cells differentiate to become plasmablasts and plasma cells, CD20 is lost but CD19 +> remains, as CD38/CD138 is acquired" +— Griffin & Rothstein 2012 (PMID: 22654880; DOI: 10.3389/fimmu.2012.00122) + +> "ASC responses in ICU-C patients were highly enriched in more mature CD138+ cells relative +> to both OUT-C and HDs." +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "**CD138neg ASC**: CD138−" and "**CD138pos ASC**: CD138+" [gating labels distinguishing +> plasmablasts from plasma cells within the CD19+CD27+CD38hi ASC gate] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +--- + +### CD21 / Complement Receptor 2 (DN B cell subtype marker — positive on BDN1/BDN4, negative on BDN2/BDN3) + +Context: CD21 (complement receptor 2, CR2) is expressed on follicular and marginal-zone +B cells. Among double-negative (IgD−CD27−) B cells, CD21 expression subdivides BDN1 +and BDN4 (CD21+) from BDN2 and BDN3 (CD21−). CD21 negativity co-occurs with CD11c +positivity in the extrafollicular BDN2 subset. + +> "DN1: CD11c− CD21+" / "DN2: CD11c+ CD21−" / "DN3: CD11c− CD21−" [gating table] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "CD19+IgD−CD27−CD21+ CD11c− T-bet− CXCR5+" [DN1 phenotype, Table 1] and +> "CD19+IgD−CD27−CD21− CD11c+ T-bet+CXCR5−" [DN2 phenotype] and +> "CD19+IgD−CD27−CD21− CD11c−" [DN3 phenotype] +— Sachinidis & Garyfallos 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) + +> "The gradual loss of CD10, CD5, and IgM and the upregulation of CD22, CD44, CD21, and +> CD23 as cells progress from immature to transitional (TI to T2 to T3) to mature naïve cells" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) +[CD21 upregulation during B cell maturation provides additional context for CD21 as a +maturity marker, contrasting with its loss in BDN2/BDN3] + +--- + +### CD11c / ITGAX (DN B cell type 2 marker; also expressed on T-bet+ age-associated B cells) + +Context: CD11c (integrin alpha-X, ITGAX) is a hallmark of the extrafollicular BDN2 subset +of double-negative B cells and of age-associated B cells (ABCs) / atypical memory B cells +observed in malaria, SLE, and COVID-19. Among DN B cells, CD11c positivity defines BDN2 +exclusively; BDN1, BDN3, and BDN4 are all CD11c−. + +> "DN2 B cells are a unique double-negative population (IgD−CD27−) that displays +> extrafollicular characteristics, such as the lack of CXCR5 and CD62L expression." +— Sachinidis & Garyfallos 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) + +> "CD19+IgD−CD27−CD21− CD11c+ T-bet+CXCR5−" [DN2 phenotype, Table 1] +— Sachinidis & Garyfallos 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) + +> "DN1: CD11c− CD21+" / "DN2: CD11c+ CD21−" / "DN3: CD11c− CD21−" [gating table] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "six distinct circulating MBC phenotypes were found that were definable based on the +> combinatorial expression of CD27, CD73, CD95, CD19, CD11c, and the CD45 isoform CD45RB" +— McGrath, Li & Wilson 2022 (PMID: 35393268; DOI: 10.1016/j.it.2022.03.005) + +--- + +### CD185 / CXCR5 (DN B cell type 1/4 marker; also marks follicular B cells) + +Context: CXCR5 (CXC chemokine receptor 5, CD185) directs lymphocytes into germinal +centres in secondary lymphoid organs (follicular homing). Among double-negative B cells, +CXCR5 positivity is the key feature of BDN1 (and by extension BDN4), which are follicular- +like. BDN2 and BDN3 are CXCR5−, reflecting their extrafollicular nature. + +> "The CXCR5+ subgroup, now known as DN1, is the DN sub-population that expands in +> elderly healthy individuals, while the CXCR5- subgroup constitutes the extrafollicular +> DN2 subset." +— Sachinidis & Garyfallos 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) + +> "DN2 B cells are a unique double-negative population (IgD−CD27−) that displays +> extrafollicular characteristics, such as the lack of CXCR5 and CD62L expression." +— Sachinidis & Garyfallos 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) + +> "CD19+IgD−CD27−CD21+ CD11c− T-bet− CXCR5+" [DN1 phenotype, Table 1] +— Sachinidis & Garyfallos 2021 (PMID: 34964023; DOI: 10.31138/mjr.32.3.192) + +> "CD21lo Tr cells expressed higher levels of markers of the early transitional compartment +> (IgM, CD24, CD10), but less CD21 and CXCR5" +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "a decrease in follicular homing predisposition through CXCR5 and a corresponding increase +> in CXCR3" [describing extrafollicular B cell responses in COVID-19 severity] +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +--- + +### CD14, CD3, CD56 (exclusion markers for B cell gate) + +Context: CD14 (monocyte), CD3 (T cell), and CD56 (NK cell) markers are used in a "dump +channel" to exclude non-B lineage cells from the B cell gate. The SOULCAP B cell gate +additionally excludes CD33 (myeloid) and CD64 (high-affinity Fc receptor on macrophages). +The quotes below confirm CD14, CD3, and CD56 usage as negative-selection markers; +direct verbatim evidence for CD33 and CD64 was not found in the accessible papers (see +below). + +> "B cells were enriched using negative selection of CD2, CD3, CD14, CD16, CD36, CD42b, +> CD56, CD66b and CD123." +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "Cells were gated as CD3−CD14−CD16−CD19+CD38+CD27+ single live cells" +— Woodruff et al. 2020 (PMID: 33028979; DOI: 10.1038/s41590-020-00814-z) + +> "a population of enriched B cells (CD3−CD14−) was collected" +— Martin et al. 2016 (PMID: 27994589; DOI: 10.3389/fimmu.2016.00546) + +--- + +## Markers with no direct evidence found + +- **CD33 / Siglec-3**: No verbatim sentence found in the five accessible papers. CD33 is a + myeloid-lineage antigen used in the SOULCAP B cell dump channel. Its use as a B cell + exclusion marker is standard practice in high-parameter flow cytometry panels but was not + stated verbatim in the fetched texts. +- **CD64 / FcγRI (FCGR1A)**: No verbatim sentence found. CD64 marks monocytes and + macrophages and is included in the SOULCAP B cell gate as an exclusion marker. As with + CD33, its use is established convention but was absent from the open-access papers + retrieved here. +- **BDN4 IgE+ subtype**: No verbatim characterisation found of a fourth DN B cell subset + distinguished by IgE surface expression. All three papers covering DN B cells (Woodruff + et al. 2020, Sachinidis & Garyfallos 2021, and the Frontiers transitional B cell review) + describe a three-subset model (DN1/DN2/DN3). The SOULCAP BDN4 definition + (CD21+ CD11c− CXCR5+ IgE+) extends the DN1 phenotype by IgE surface staining; + literature support for this specific IgE-positive split was not found in the accessible + open-access corpus. A targeted search of Wehr et al. or Sanz et al. publications (which + first proposed 4-subset DN B cell classifications) may supply this evidence. + +--- + +## Paywalled or inaccessible papers + +| Paper | Reason inaccessible | +|-------|---------------------| +| Surowiecki et al. / Nat Immunol 2021 (PMID 34725481) — "Surface phenotypes of naive and memory B cells" | EuropePMC returned navigation HTML only; Nature.com requires authentication | +| Comprehensive analyses of B-cell compartments / Blood 2020 (DOI 10.1182/blood.2019002782) | ashpublications.org returned HTTP 403 Forbidden | +| Double-negative B cells: an under-recognized effector memory B cell subset / Clin Exp Immunol 2021 (PMID 34075582) | Wiley Online Library returned HTTP 402 Payment Required | +| Human B1 cells in umbilical cord and adult peripheral blood / JEM 2011 (PMID 21199954) | Not attempted (Rockefeller UP / rupress.org is gated) | + +--- + +## Sources + +| PMID | DOI | Title | Authors | Year | Journal | Access | +|------|-----|-------|---------|------|---------|--------| +| 27994589 | 10.3389/fimmu.2016.00546 | Transitional B Cells in Early Human B Cell Development – Time to Revisit the Paradigm? | Martin VG, Wu Y-CB, Townsend CL et al. | 2016 | Front Immunol | Open (Frontiers) | +| 35393268 | 10.1016/j.it.2022.03.005 | Memory B cell diversity: insights for optimized vaccine design | McGrath JJC, Li L, Wilson PC | 2022 | Trends Immunol | Open (PMC8977948) | +| 34964023 | 10.31138/mjr.32.3.192 | Double Negative (DN) B cells: A connecting bridge between rheumatic diseases and COVID-19? | Sachinidis A, Garyfallos A | 2021 | Mediterr J Rheumatol | Open (PMC8693305) | +| 33028979 | 10.1038/s41590-020-00814-z | Extrafollicular B cell responses correlate with neutralizing antibodies and morbidity in COVID-19 | Woodruff MC, Ramonell RP, Nguyen DC et al. | 2020 | Nat Immunol | Open (PMC7739702) | +| 22654880 | 10.3389/fimmu.2012.00122 | Human B1 Cell Frequency: Isolation and Analysis of Human B1 Cells | Griffin DO, Rothstein TL | 2012 | Front Immunol | Open (Frontiers) | diff --git a/reports/literature/gdt_mait_markers.md b/reports/literature/gdt_mait_markers.md new file mode 100644 index 0000000..5ae13df --- /dev/null +++ b/reports/literature/gdt_mait_markers.md @@ -0,0 +1,209 @@ +# Gamma-Delta T Cell and MAIT Cell Marker Literature Support + +Evidence for SOULCAP γδ T cell and MAIT cell marker definitions, extracted verbatim from open-access papers. All blockquotes are copied character-for-character from the source. Paywalled papers (OMIP-084, OMIP-020, Nature Immunology 2023) are noted in the Sources table but no quotes are drawn from them. + +--- + +## Part I: Gamma-Delta T Cell Markers + +### CD3 and TCRγδ (required — pan-γδ T cell markers) + +Context: γδ T cells express CD3 and the γδ form of the TCR. The two T cell lineages — αβ and γδ — are mutually exclusive at the TCR level, so TCRγδ staining with CD3 uniquely marks this lineage. + +> "Cytobank 5.0 was used (following quality control and data scaling) to gate live/CD3+/γδ TCR+ cells." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "As γδ T cells are less likely to cause graft-versus-host disease (GvHD) than their αβ counterparts" +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "γδ T cells are a highly versatile immune lineage involved in host defense and homeostasis, but questions remain around their heterogeneity, precise function and role during health and disease." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +--- + +### γδ T cell subsets — overview (three Vδ populations) + +Context: SOULCAP defines Vδ1, Vδ2, Vδ3, Vγ9, Vγ9Vδ1, Vγ9Vδ2, and pan-γδ populations. The three-subset Vδ-based classification is standard in the literature. + +> "The γδ T cells are typically classified into three primary subsets based on their δ chain usage: Vδ1+, Vδ2+, and Vδ3+" +— Laub et al. 2025 (PMID:40746558; DOI:10.3389/fimmu.2025.1618393) + +> "Traditionally, γδ T cells existed as three populations based on δ chain expression. Vδ1 cells predominantly reside in mucosal sites and epithelia, while Vδ2 cells comprise 50–90% of γδ T cells in the circulation." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +--- + +### TCR Vδ2 / TRDV2 (major peripheral blood γδ subset marker) + +Context: Vδ2-expressing cells — usually paired with Vγ9 — are the dominant γδ T cell subset in peripheral blood of healthy adults. Identification of the SOULCAP "Vd2" cell type (non-Vγ9 Vδ2) requires TCR Vδ2+ combined with Vγ9- and Vδ1-. + +> "Vδ2 cells comprise 50–90% of γδ T cells in the circulation and are both effectors and antigen-presenting cells (APCs)." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "The most abundant T cell subtype in human peripheral blood is the Vδ2+ T cell." +— Wang et al. 2026 (PMID:42344895; DOI:10.3389/fimmu.2026.1827307) + +> "It accounts for approximately 50% to 95% of total γδ T cells" +— Wang et al. 2026 (PMID:42344895; DOI:10.3389/fimmu.2026.1827307) + +> "Vδ2+ T cells, represented by Vγ9Vδ2 T cells, the dominant circulating subset in humans" +— Laub et al. 2025 (PMID:40746558; DOI:10.3389/fimmu.2025.1618393) + +> "Vδ1− cells are likely to be the predominant Vδ2+ in circulation" +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +--- + +### TCR Vγ9 / TRGV9 (paired with Vδ2 in the dominant peripheral blood subset) + +Context: The Vγ9Vδ2 heterodimer is the defining TCR of the dominant blood γδ T cell subset. SOULCAP uses TCR Vγ9 positivity as a required marker for the "Vg9 Vd2" and "Vg9" cell types, and optionally ("+/-") for "Vd1". + +> "Most predominantly, it pairs with the Vγ9 chain forming a functional heterodimer, Therefore, this cell is also known as Vγ9Vδ2 T cell" +— Wang et al. 2026 (PMID:42344895; DOI:10.3389/fimmu.2026.1827307) + +> "Vδ2+ γδ T cells, the dominant circulating subset in humans, are activated by non-peptidic phosphorylated intermediates of the mevalonate pathway." +— Laub et al. 2025 (PMID:40746558; DOI:10.3389/fimmu.2025.1618393) + +--- + +### TCR Vδ1 / TRDV1 (tissue-resident subset; paired with various Vγ chains) + +Context: Vδ1+ cells predominate in mucosal and epithelial tissues and are the minor γδ T cell subset in blood. SOULCAP defines "Vd1" (TCRgd+ TCR V delta 1+, V delta 2-, V gamma 9+/-) and "Vg9 Vd1" (both V delta 1+ and V gamma 9+). + +> "Vδ1+ T cells are mainly found in the mucosal tissues (intestinal tissues) and epithelial tissues (such as skin)" +— Wang et al. 2026 (PMID:42344895; DOI:10.3389/fimmu.2026.1827307) + +> "Vδ1+ T cells are the primary tissue-resident γδ T cell subset" +— Wang et al. 2026 (PMID:42344895; DOI:10.3389/fimmu.2026.1827307) + +> "The Vδ1 chain can pair with multiple γ chains (e.g., Vγ2, Vγ3, Vγ4)" +— Wang et al. 2026 (PMID:42344895; DOI:10.3389/fimmu.2026.1827307) + +> "Vδ1+ cells maintain a predominant population of TEM/TEMRA γδ T cells" +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "Vδ1+ and Vδ1− (as a percentage of γδ T cells) of 30.6% (± SD 27%) and 69.2% (± SD 27%) respectively." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +--- + +### CD161 (NKR-P1 / KLRB1 — used to define CD161+ γδ T cell subsets) + +Context: CD161 (also called NKR-P1 or KLRB1) is differentially expressed across γδ T cell subsets and serves as a key marker distinguishing subpopulations, particularly Vδ1- (Vδ2-enriched) from Vδ1+ cells. + +> "γδ T cells were divided into two populations based on Vδ1 expression. Each population was subgated based on CD45RA and CD27 expression to differentiate naïve and memory cells and then gated based on CD161, CD4 and CD8 expression." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "Comparison of CD161 expression between naïve and memory Vδ1+ and Vδ1− populations revealed a significant difference in both TEM cells and TCM cells (p < 0.0001), with Vδ1− cells having the highest surface expression of CD161." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "Both methods show CD161 as a primary differentiating phenotypic marker for Vδ cell subsets." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "Overall, the pattern of marker expression on the eight clusters show that CD161 plays a central role in the differentiation of γδ T cell subtypes." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "CD161 expression on γδ T cells is associated with enhanced IFN-γ and IL-17 production and enhanced endothelial transmigration." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +> "CD161 is a C-type lectin-like membrane receptor expressed at high levels on NK, NKT, Th17, Mucosa Associated Invariant T cells (MAITs), non-MAIT CD8+, tissue-resident memory cells (TRMs)." +— Karunathilaka et al. 2022 (PMID:35193613; DOI:10.1186/s12979-022-00269-w) + +--- + +## Part II: MAIT Cell Markers + +### CD3 and TCRαβ (required positive — MAIT cells are αβ T cells) + +Context: MAIT cells are a subset of αβ T cells. They express CD3 as part of the TCR complex, and their TCR comprises αβ chains (TRAV1-2/TRAJ33 α-chain paired with restricted TRBV β-chains), not γδ chains. + +> "Human MAIT cells express an invariant TCRα chain comprising TRAV1-2 joined to TRAJ33 with a restricted TCRβ chain TRBV6 and TRBV20." +— Azad et al. 2025 (PMID:41511352; DOI:10.3390/cells15010069) + +> "demonstrated the flow cytometry using CD3, CD4, CD8, TCRβ, MR1 tetramer" +— Cai et al. 2026 (PMID:41804231; DOI:10.1111/cpr.70194) + +> "MAIT cells belong to a population of 'unconventional' T cells which also include gamma delta (gd) T cells and invariant natural killer (iNKT) cells." +— Azad et al. 2025 (PMID:41511352; DOI:10.3390/cells15010069) + +--- + +### TCR Vα7.2 / TRAV1-2 (required — invariant α-chain of MAIT TCR) + +Context: The invariant TRAV1-2 (Vα7.2) gene segment defines the MAIT cell α-chain in humans. Vα7.2 staining is the primary surrogate marker used alongside CD161 in flow cytometry panels. The alias "Vα7.2" refers to the protein product of the TRAV1-2 gene. + +> "the semi-invariant conserved MAIT TCR predominantly utilizes TRAV1-2 (Vα7.2 in humans)" +— Laub et al. 2025 (PMID:40746558; DOI:10.3389/fimmu.2025.1618393) + +> "their semi-invariant TCR typically comprises a concrete TCRα chain (encoded by *TRAV1-2/TRAJ33* genes)" +— García-Escribano et al. 2026 (PMID:42433370; DOI:10.3389/fimmu.2026.1852383) + +> "In humans, the majority of MAIT cells are defined as CD8+CD161+Vα7.2+ T cells" +— García-Escribano et al. 2026 (PMID:42433370; DOI:10.3389/fimmu.2026.1852383) + +> "Circulating MAIT cells from healthy donors can be identified using surrogate set of markers TCRVα7.2+ CD161+ (and/or CD26+)." +— Azad et al. 2025 (PMID:41511352; DOI:10.3390/cells15010069) + +> "Using TCR Vα7.2 and CD161, we identified MAIT cells in human liver tissues" +— Cai et al. 2026 (PMID:41804231; DOI:10.1111/cpr.70194) + +--- + +### CD161 (required positive — pan-MAIT marker; co-expressed with Vα7.2) + +Context: CD161 (encoded by KLRB1) is expressed on essentially all MAIT cells and is used alongside Vα7.2 to identify bona fide MAIT cells. A caveat is that CD161 can also mark other innate-like T cell populations (NKT, Th17, some CD8+ T cells) and can be downregulated upon activation, so it must be used in combination with Vα7.2 or MR1 tetramer. + +> "Human MAIT cells were gated as Zombie−CD14−CD19−CD8α+CD161+Vα7.2+ cells" +— García-Escribano et al. 2026 (PMID:42433370; DOI:10.3389/fimmu.2026.1852383) + +> "Gene transcriptomic analysis has identified MAIT cell-specific markers, including TRAV1-2+ TCR, CD161, PLZF, and IL-18Rα" +— Laub et al. 2025 (PMID:40746558; DOI:10.3389/fimmu.2025.1618393) + +> "Surrogate markers, especially CD161 may lead to the inconsistent identification of MAIT cells, as CD161 can be downregulated in activation." +— Azad et al. 2025 (PMID:41511352; DOI:10.3390/cells15010069) + +> "annotated cluster 2 into MAIT according to the high expression of KLRB1, SLC4A10, ZBTB16, RORA, and RORC" +— Cai et al. 2026 (PMID:41804231; DOI:10.1111/cpr.70194) + +--- + +### MR1 Tetramer (alternative MAIT identification; more specific than Vα7.2 alone) + +Context: Tetramers of MR1 loaded with 5-OP-RU (a riboflavin metabolite) bind directly to the MAIT TCR and are more specific than Vα7.2 staining alone. MR1 tetramers identify MAIT cells regardless of CD161 expression level. The ligands for MR1 include microbial riboflavin metabolites, folate derivatives, and other small molecules. + +> "The most specific method of identifying MAIT cells is by using MR1-5-OP-RU tetramers in flow cytometry." +— Azad et al. 2025 (PMID:41511352; DOI:10.3390/cells15010069) + +> "MAIT cells were isolated from PBMCs using a 5-OP-RU-loaded PE-conjugated MR1 tetramer" +— García-Escribano et al. 2026 (PMID:42433370; DOI:10.3389/fimmu.2026.1852383) + +> "performed longitudinal monitoring of circulating MAIT cells using MR1‐tetramer staining" +— Cai et al. 2026 (PMID:41804231; DOI:10.1111/cpr.70194) + +> "The MAIT cell TCR recognizes a series of MR1-binding ligands which includes endogenous bile acids, drug molecules, folate, and riboflavin derivatives" +— Azad et al. 2025 (PMID:41511352; DOI:10.3390/cells15010069) + +--- + +## Markers with no direct evidence found + +- **TCR V delta 3 (TRDV3) — Vδ3 T cells**: Vδ3 is enumerated as a subset category (e.g., "Vδ1+, Vδ2+, and Vδ3+" in Laub et al. 2025) but no open-access paper was found that provides verbatim gating or phenotyping criteria for the Vδ3 population specifically. SOULCAP defines Vδ3 by exclusion: TCRgd+ Vδ1- Vδ2- Vγ9-. +- **TCR V gamma 9 in Vδ1 context (Vγ9Vδ1 pairing)**: The literature confirms Vδ1 pairs with multiple Vγ chains (Vγ2, Vγ3, Vγ4; Wang et al. 2026) and that Vδ2 pairs predominantly with Vγ9 (Wang et al. 2026). No open-access quote was found explicitly characterising the Vγ9Vδ1 minor subset, which SOULCAP lists as a separate cell type. +- **TCRαβ exclusion on γδ T cells (explicit)**: The literature confirms γδ T cells are the αβ counterpart's alternative lineage (Karunathilaka et al. 2022: "less likely to cause GvHD than their αβ counterparts"), and SOULCAP's TCRgd panel gates on TCRγδ+ or TCRαβ- to exclude αβ T cells, but no open-access paper was found with a verbatim gating statement using "TCRαβ-" to define γδ T cells. +- **CD26 as supplementary MAIT marker**: Mentioned in one paper as an optional co-marker ("TCRVα7.2+ CD161+ (and/or CD26+)"; Azad et al. 2025) but not included in SOULCAP's current MAIT definition. + +--- + +## Sources + +| PMID | DOI | Title | Authors | Year | Journal | Access | +|------|-----|-------|---------|------|---------|--------| +| 35193613 | 10.1186/s12979-022-00269-w | CD161 expression defines new human γδ T cell subsets | Karunathilaka A et al. | 2022 | Immunity & Ageing | Open (PMC8862246) | +| 40746558 | 10.3389/fimmu.2025.1618393 | Unconventional T cells in anti-cancer immunity | Laub A et al. | 2025 | Frontiers in Immunology | Open (PMC12310680) | +| 42344895 | 10.3389/fimmu.2026.1827307 | Harnessing Vδ1+ T cells for next-generation immunotherapy | Wang F et al. | 2026 | Frontiers in Immunology | Open (PMC13286967) | +| 41511352 | 10.3390/cells15010069 | MAIT Cells in Liver Disease | Azad AI et al. | 2025 | Cells (MDPI) | Open (PMC12785784) | +| 42433370 | 10.3389/fimmu.2026.1852383 | Synergistic TCR-independent action of IL-33 and IL-12 drive a potent IFNγ secretory program in human circulating MAIT cells | García-Escribano C et al. | 2026 | Frontiers in Immunology | Open (PMC13349841) | +| 41804231 | 10.1111/cpr.70194 | Single Cell Multi-Omics Revealing the Important Role of MR1 Mediated MAIT Cells in Maintaining Rejection for Liver Transplantation | Cai H et al. | 2026 | Cell Proliferation | Open (PMC13325667) | +| — | 10.1002/cyto.a.24564 | OMIP-084: 28-color panel for human γδ T cell subsets | — | 2022 | Cytometry Part A | **Paywalled (402)** | +| — | 10.1002/cyto.a.22470 | OMIP-020: Phenotypic characterization of human γδ T cells | — | 2013 | Cytometry Part A | **Paywalled (402)** | +| — | 10.1038/s41590-023-01575-1 | Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity | — | 2023 | Nature Immunology | **Paywalled (redirect to auth)** | From eb28a0f06c5cf4d77dc7549975ac2c7fa4954938 Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Sat, 18 Jul 2026 21:20:15 -0400 Subject: [PATCH 6/8] docs: record upstream CL issues filed for #13 NKT cell naming CL:4052055 -> obophenotype/cell-ontology#3663 CL:0000814 -> obophenotype/cell-ontology#3664 Co-Authored-By: Claude Sonnet 4.6 --- ROADMAP.md | 2 +- reports/cl_term_issues.md | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/ROADMAP.md b/ROADMAP.md index ea0ea0b..27c3bce 100644 --- a/ROADMAP.md +++ b/ROADMAP.md @@ -131,7 +131,7 @@ upstream to `obophenotype/cell-ontology`. | Issue | Terms | Status | |-------|-------|--------| -| [#13 NKT cell naming](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/13) | CL:4052055 → "CD56-positive T cell, human"; CL:0000814 → "iNKT cell" | Open — not yet filed upstream | +| [#13 NKT cell naming](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/13) | CL:4052055 → "CD56-positive T cell, human"; CL:0000814 → "iNKT cell" | Filed upstream: [CL#3663](https://github.com/obophenotype/cell-ontology/issues/3663), [CL#3664](https://github.com/obophenotype/cell-ontology/issues/3664) | --- diff --git a/reports/cl_term_issues.md b/reports/cl_term_issues.md index b992d28..47b5f0b 100644 --- a/reports/cl_term_issues.md +++ b/reports/cl_term_issues.md @@ -15,7 +15,7 @@ See [CLAUDE.md](../CLAUDE.md) for project conventions. **Repo issue:** [#13 NKT cell naming](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/13) **Filed by:** Kelly Lundsten · 2026-07-08 **Reference:** [PMC6647187](https://pmc.ncbi.nlm.nih.gov/articles/PMC6647187/) -**Status:** Open — not yet filed upstream to `obophenotype/cell-ontology` +**Status:** Filed upstream — awaiting CL maintainer review #### CL:4052055 — "Mature NK T cell, human" @@ -50,8 +50,9 @@ TCRVβ11+) correspond specifically to the iNKT lineage. Renaming to "iNKT cell" and scoping the definition accordingly prevents conflation with vNKT and CD56+ T cells. -**Upstream action needed:** File issue against `obophenotype/cell-ontology` -requesting label change + definition update for both terms. +**Upstream issues filed:** +- CL:4052055 → https://github.com/obophenotype/cell-ontology/issues/3663 +- CL:0000814 → https://github.com/obophenotype/cell-ontology/issues/3664 --- From 58bedd0546cfed8f4f56fee6873d05c16ed5c6ea Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Sun, 19 Jul 2026 15:54:12 -0400 Subject: [PATCH 7/8] docs: record upstream CL issue filed for #12 monocyte corrections CL:0000576/0000860/0002393/0000875 -> obophenotype/cell-ontology#3665 Co-Authored-By: Claude Sonnet 4.6 --- reports/cl_term_issues.md | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/reports/cl_term_issues.md b/reports/cl_term_issues.md index 47b5f0b..e80205a 100644 --- a/reports/cl_term_issues.md +++ b/reports/cl_term_issues.md @@ -54,6 +54,29 @@ cells. - CL:4052055 → https://github.com/obophenotype/cell-ontology/issues/3663 - CL:0000814 → https://github.com/obophenotype/cell-ontology/issues/3664 +### Monocyte corrections — CL:0000576, CL:0000860, CL:0002393, CL:0000875 + +**Repo issue:** [#12 Clarification of monocytes](https://github.com/Cellular-Semantics/SOULCAP_CL_Mapping/issues/12) +**Filed by:** Kelly Lundsten +**Status:** Filed upstream — awaiting CL maintainer review + +**Upstream issue filed:** +- CL:0000576/0000860/0002393/0000875 → https://github.com/obophenotype/cell-ontology/issues/3665 + +#### Changes requested + +1. **Typo fix** — `CX3CCR1` and `CXCCR1` → `CX3CR1` in CL:0000576 and CL:0000875 +2. **Duplicated description** — remove duplicate block from CL:0000860 (classical monocyte) +3. **Mouse marker string** (CL:0000576) — replace `F4/80-mid, GR1-low` with `CD64 lo/- F4/80 lo/- MHCII lo/- CD3- CD19- B220- CD11b+/hi Ly-6G- CD317- Siglec-F- Ly-6C+/- CX3CR1+ CD11c+/- CD49b+/- CD192+/-`; rationale: GR-1 recognises both Ly-6C and Ly-6G; monocytes are Ly-6G− and Ly-6C+/− +4. **Human marker string** (CL:0000576) — replace CD192/CX3CR1 as pan-monocyte markers with `CD45+ CD66b- CD3- CD19- CD56- CD123 lo/- CD33+ CD11c lo/+ HLA-DR lo/+ CD14+/- CD16+/-`; CD192/CX3CR1 are subset discriminators, not pan-monocyte gates; all monocytes are not CD14+ +5. **Tri-subset markers** per Ziegler-Heitbrock et al. 2010 (PMID:20628149; DOI:10.1182/blood-2010-02-258558): + +| Term | CL ID | Correct markers | +|------|-------|-----------------| +| Classical monocyte | CL:0000860 | CD14^hi CD16^− CD11c^lo HLA-DR^lo | +| Intermediate monocyte | CL:0002393 | CD14^hi/+ CD16^+/hi CD11c^hi HLA-DR^hi | +| Non-classical monocyte | CL:0000875 | CD14^lo/− CD16^hi CD11c^hi HLA-DR^+ | + --- ## Resolved issues From cb6993f74f7a78259136ed27fc8881b4dcfff1bd Mon Sep 17 00:00:00 2001 From: s28ale-maker Date: Tue, 21 Jul 2026 14:47:11 -0400 Subject: [PATCH 8/8] fix: strip UniProt isoform suffixes before Monarch lookup in soulcap-hgnc MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Isoform-suffixed accessions like UniProtKB:P16871-1 were sent to the Monarch Node Normalizer verbatim; Monarch only resolves canonical accessions (P16871). Adding strip_isoform_suffix() and applying it in collect_pr_mappings() raises HGNC coverage from 3919 to 4084/4517 rows, resolving CD34, CD127, CD56, CD117, NKp46, NKp44, CD161 and others. Closes #9 (remaining 36 unmapped rows are mouse-specific PRO terms or rare human proteins Monarch cannot resolve — documented in TSV notes). Co-Authored-By: Claude Sonnet 4.6 --- reports/cl_pro_relationships.tsv | 330 ++++++++++++++--------------- src/soulcap_cl_mapping/hgnc_map.py | 27 ++- tests/test_hgnc_map.py | 32 +++ 3 files changed, 223 insertions(+), 166 deletions(-) diff --git a/reports/cl_pro_relationships.tsv b/reports/cl_pro_relationships.tsv index de37993..472f331 100644 --- a/reports/cl_pro_relationships.tsv +++ b/reports/cl_pro_relationships.tsv @@ -404,7 +404,7 @@ CL:0000624 CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part p CL:0000625 CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000625 CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000625 CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000625 CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000625 CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000632 hepatic stellate cell RO:0002104 has plasma membrane part positive True PR:000007939 glial fibrillary acidic protein UniProtKB:P14136 UniProtKB:P03995 HGNC:4235 GFAP CL:0000743 hypertrophic chondrocyte RO:0002292 expresses positive True PR:000005693 collagen alpha-1(X) chain UniProtKB:Q03692 UniProtKB:Q05306 HGNC:2185 COL10A1 CL:0000754 type 2 cone bipolar cell (sensu Mus) RO:0002292 expresses positive True PR:P50481 LIM/homeobox protein Lhx3 (mouse) UniProtKB:P50481-1; UniProtKB:P50481-2; UniProtKB:P50481 UniProtKB:P50481 @@ -608,14 +608,14 @@ CL:0000794 CD8-positive, alpha-beta cytotoxic T cell BFO:0000051 has part positi CL:0000794 CD8-positive, alpha-beta cytotoxic T cell BFO:0000051 has part positive True PR:000003466 perforin-1 UniProtKB:P14222 UniProtKB:P10820 HGNC:9360 PRF1 CL:0000794 CD8-positive, alpha-beta cytotoxic T cell BFO:0000051 has part positive True PR:000003499 granzyme B UniProtKB:P10144 IUPHARobj:2369 HGNC:4709 GZMB CL:0000794 CD8-positive, alpha-beta cytotoxic T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000794 CD8-positive, alpha-beta cytotoxic T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000794 CD8-positive, alpha-beta cytotoxic T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000795 CD8-positive, alpha-beta regulatory T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000795 CD8-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000795 CD8-positive, alpha-beta regulatory T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000795 CD8-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000795 CD8-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000796 CD8-alpha-beta-positive, alpha-beta intraepithelial T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000796 CD8-alpha-beta-positive, alpha-beta intraepithelial T cell RO:0002104 has plasma membrane part positive True PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000796 CD8-alpha-beta-positive, alpha-beta intraepithelial T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000796 CD8-alpha-beta-positive, alpha-beta intraepithelial T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000802 CD8-alpha alpha positive, gamma-delta intraepithelial T cell RO:0002104 has plasma membrane part positive True PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000803 CD4-negative CD8-negative gamma-delta intraepithelial T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A @@ -625,7 +625,7 @@ CL:0000805 immature single positive thymocyte CL:4030046 lacks_plasma_membrane_p CL:0000805 immature single positive thymocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000805 immature single positive thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000805 immature single positive thymocyte RO:0002104 has plasma membrane part positive True PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000805 immature single positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000805 immature single positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000806 DN2 thymocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000806 DN2 thymocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0000806 DN2 thymocyte RO:0002104 has plasma membrane part positive True PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) UniProtKB:P16070 UniProtKB:P15379 HGNC:1681 CD44 @@ -641,13 +641,13 @@ CL:0000808 DN4 thymocyte CL:4030046 lacks_plasma_membrane_part negative False PR CL:0000809 double-positive, alpha-beta thymocyte RO:0002104 has plasma membrane part positive True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000809 double-positive, alpha-beta thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000809 double-positive, alpha-beta thymocyte RO:0002104 has plasma membrane part positive True PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000809 double-positive, alpha-beta thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000809 double-positive, alpha-beta thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000810 CD4-positive, alpha-beta thymocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000810 CD4-positive, alpha-beta thymocyte RO:0002104 has plasma membrane part positive True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000811 CD8-positive, alpha-beta thymocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000811 CD8-positive, alpha-beta thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000811 CD8-positive, alpha-beta thymocyte RO:0002104 has plasma membrane part positive True PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000811 CD8-positive, alpha-beta thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000811 CD8-positive, alpha-beta thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000814 mature NK T cell RO:0002104 has plasma membrane part positive True PR:000001874 KLRB1-like protein PIRSF:PIRSF038804 CL:0000816 immature B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0000816 immature B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -663,13 +663,13 @@ CL:0000818 transitional stage B cell RO:0002104 has plasma membrane part positiv CL:0000819 B-1 B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0000819 B-1 B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0000819 B-1 B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000819 B-1 B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000819 B-1 B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000819 B-1 B cell RO:0002104 has plasma membrane part positive True PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000819 B-1 B cell RO:0002104 has plasma membrane part positive True PR:000001879 leukosialin CD43 (related) UniProtKB:P16150 UniProtKB:P15702 PIRSF:PIRSF001994 HGNC:11249 SPN CL:0000820 B-1a B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0000820 B-1a B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0000820 B-1a B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000820 B-1a B cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000820 B-1a B cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000820 B-1a B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000820 B-1a B cell RO:0002104 has plasma membrane part positive True PR:000001839 T-cell surface glycoprotein CD5 CD5 (label) UniProtKB:P06127 UniProtKB:P13379 HGNC:1685 CD5 CL:0000820 B-1a B cell RO:0002104 has plasma membrane part positive False PR:000001879 leukosialin CD43 (related) UniProtKB:P16150 UniProtKB:P15702 PIRSF:PIRSF001994 HGNC:11249 SPN @@ -677,7 +677,7 @@ CL:0000821 B-1b B cell CL:4030046 lacks_plasma_membrane_part negative False PR:0 CL:0000821 B-1b B cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001839 T-cell surface glycoprotein CD5 CD5 (label) UniProtKB:P06127 UniProtKB:P13379 HGNC:1685 CD5 CL:0000821 B-1b B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0000821 B-1b B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000821 B-1b B cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000821 B-1b B cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000821 B-1b B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000821 B-1b B cell RO:0002104 has plasma membrane part positive False PR:000001879 leukosialin CD43 (related) UniProtKB:P16150 UniProtKB:P15702 PIRSF:PIRSF001994 HGNC:11249 SPN CL:0000822 B-2 B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E @@ -696,7 +696,7 @@ CL:0000825 pro-NK cell CL:4030046 lacks_plasma_membrane_part negative True PR:00 CL:0000825 pro-NK cell CL:4030046 lacks_plasma_membrane_part negative True PR:000002065 mast/stem cell growth factor receptor CD117 (exact) UniProtKB:P10721 UniProtKB:P05532 IUPHARobj:1805; PIRSF:PIRSF500951 HGNC:6342 KIT CL:0000825 pro-NK cell RO:0002104 has plasma membrane part positive True PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0000825 pro-NK cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000825 pro-NK cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000825 pro-NK cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000825 pro-NK cell RO:0002104 has plasma membrane part positive True PR:000001381 interleukin-2 receptor subunit beta CD122 (exact) UniProtKB:P14784 UniProtKB:P16297 IUPHARobj:1696 HGNC:6009 IL2RB CL:0000825 pro-NK cell RO:0002104 has plasma membrane part positive True PR:000001898 neprilysin CD10 (exact) UniProtKB:P08473 UniProtKB:Q61391 IUPHARobj:1611; PIRSF:PIRSF501074 HGNC:7154 MME CL:0000826 pro-B cell BFO:0000051 has part positive True PR:000001903 paired box protein PAX-5 UniProtKB:Q02548 UniProtKB:Q02650 HGNC:8619 PAX5 @@ -776,7 +776,7 @@ CL:0000843 follicular B cell CL:4030046 lacks_plasma_membrane_part negative Fals CL:0000843 follicular B cell CL:4030046 lacks_plasma_membrane_part negative True PR:000002037 complement component C1q receptor CD93 (exact); CDw93 (exact) UniProtKB:Q9NPY3 UniProtKB:O89103 HGNC:15855 CD93 CL:0000843 follicular B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0000843 follicular B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000843 follicular B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000843 follicular B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000843 follicular B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000843 follicular B cell RO:0002104 has plasma membrane part positive True PR:000001338 complement receptor type 2 CD21 (exact) UniProtKB:P20023 UniProtKB:P19070 PIRSF:PIRSF002484 HGNC:2336 CR2 CL:0000844 germinal center B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E @@ -853,7 +853,7 @@ CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell CL:4030046 lacks CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0000896 activated CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001318 L-selectin CD62 (exact); CD62L (exact) UniProtKB:P14151 UniProtKB:P18337 PIRSF:PIRSF002421 HGNC:10720 SELL @@ -867,7 +867,7 @@ CL:0000897 CD4-positive, alpha-beta memory T cell RO:0002104 has plasma membrane CL:0000898 naive T cell RO:0015015 has high plasma membrane amount high True PR:000001318 L-selectin CD62 (exact); CD62L (exact) UniProtKB:P14151 UniProtKB:P18337 PIRSF:PIRSF002421 HGNC:10720 SELL CL:0000898 naive T cell RO:0015016 has low plasma membrane amount low True PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) UniProtKB:P16070 UniProtKB:P15379 HGNC:1681 CD44 CL:0000898 naive T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000898 naive T cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000898 naive T cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000898 naive T cell RO:0002104 has plasma membrane part positive True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0000898 naive T cell RO:0002104 has plasma membrane part positive True PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0000899 T-helper 17 cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001207 C-X-C chemokine receptor type 3 CD183 (exact) UniProtKB:P49682 UniProtKB:O88410 IUPHARobj:70; PIRSF:PIRSF501023 HGNC:4540 CXCR3 @@ -880,12 +880,12 @@ CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell RO:0015016 has l CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000901 Tr1 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0000901 Tr1 cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000902 induced T-regulatory cell RO:0015016 has low plasma membrane amount low False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R @@ -902,22 +902,22 @@ CL:0000903 natural T-regulatory cell BFO:0000051 has part positive True PR:00000 CL:0000903 natural T-regulatory cell RO:0002104 has plasma membrane part positive False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000903 natural T-regulatory cell RO:0002104 has plasma membrane part positive True PR:000001852 cytotoxic T-lymphocyte protein 4 CD152 (related) UniProtKB:P16410 UniProtKB:P09793 IUPHARobj:2743 HGNC:2505 CTLA4 CL:0000904 central memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000904 central memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000904 central memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000904 central memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000904 central memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0000904 central memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000904 central memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000904 central memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0000904 central memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0000904 central memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0000904 central memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0000905 effector memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000905 effector memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000905 effector memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000905 effector memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0000905 effector memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000905 effector memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0000905 effector memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000905 effector memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000905 effector memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0000905 effector memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0000905 effector memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0000906 activated CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000906 activated CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 @@ -927,18 +927,18 @@ CL:0000906 activated CD8-positive, alpha-beta T cell BFO:0000051 has part positi CL:0000906 activated CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001343 CD69 molecule CD69 (label) UniProtKB:Q07108 UniProtKB:P37217 HGNC:1694 CD69 CL:0000906 activated CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000906 activated CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000906 activated CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000906 activated CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000907 central memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000907 central memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000907 central memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000907 central memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000907 central memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000907 central memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000907 central memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0000907 central memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0000907 central memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000907 central memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0000907 central memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0000907 central memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000907 central memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000907 central memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001318 L-selectin CD62 (exact); CD62L (exact) UniProtKB:P14151 UniProtKB:P18337 PIRSF:PIRSF002421 HGNC:10720 SELL CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R @@ -946,22 +946,22 @@ CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell BFO:00000 CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell RO:0002104 has plasma membrane part positive True PR:000001343 CD69 molecule CD69 (label) UniProtKB:Q07108 UniProtKB:P37217 HGNC:1694 CD69 CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell RO:0002104 has plasma membrane part positive True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000908 CD8-positive, alpha-beta cytokine secreting effector T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000909 CD8-positive, alpha-beta memory T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000909 CD8-positive, alpha-beta memory T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000909 CD8-positive, alpha-beta memory T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000909 CD8-positive, alpha-beta memory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000909 CD8-positive, alpha-beta memory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000913 effector memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000913 effector memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000913 effector memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000913 effector memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000913 effector memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0000913 effector memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000913 effector memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000913 effector memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0000913 effector memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0000913 effector memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000913 effector memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0000913 effector memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000913 effector memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000913 effector memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000914 immature NK T cell BFO:0000051 has part positive True PR:000003469 early growth response protein 2 UniProtKB:P11161 UniProtKB:P08152 HGNC:3239 EGR2 CL:0000915 CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001083 CD2 molecule CD2 (label) UniProtKB:P06729 UniProtKB:P08920 IUPHARobj:2600; PIRSF:PIRSF001984 HGNC:1639 CD2 CL:0000915 CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001839 T-cell surface glycoprotein CD5 CD5 (label) UniProtKB:P06127 UniProtKB:P13379 HGNC:1685 CD5 @@ -977,7 +977,7 @@ CL:0000917 Tc1 cell RO:0002104 has plasma membrane part positive False PR:000001 CL:0000917 Tc1 cell BFO:0000051 has part positive True PR:000001835 T-box transcription factor TBX21 UniProtKB:Q9UL17 UniProtKB:Q9JKD8 HGNC:11599 TBX21 CL:0000917 Tc1 cell BFO:0000051 has part positive True PR:000003463 eomesodermin UniProtKB:O95936 UniProtKB:O54839 HGNC:3372 EOMES CL:0000917 Tc1 cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000917 Tc1 cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000917 Tc1 cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000918 Tc2 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000918 Tc2 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001202 C-C chemokine receptor type 6 CD196 (exact) UniProtKB:P51684 UniProtKB:O54689 IUPHARobj:63 HGNC:1607 CCR6 CL:0000918 Tc2 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001207 C-X-C chemokine receptor type 3 CD183 (exact) UniProtKB:P49682 UniProtKB:O88410 IUPHARobj:70; PIRSF:PIRSF501023 HGNC:4540 CXCR3 @@ -988,19 +988,19 @@ CL:0000918 Tc2 cell RO:0002104 has plasma membrane part positive False PR:000001 CL:0000918 Tc2 cell RO:0002104 has plasma membrane part positive False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000918 Tc2 cell BFO:0000051 has part positive True PR:000001941 trans-acting T-cell-specific transcription factor GATA-3 UniProtKB:P23771 UniProtKB:P23772 HGNC:4172 GATA3 CL:0000918 Tc2 cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000918 Tc2 cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000918 Tc2 cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000919 CD8-positive, CD25-positive, alpha-beta regulatory T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000919 CD8-positive, CD25-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000919 CD8-positive, CD25-positive, alpha-beta regulatory T cell BFO:0000051 has part positive True PR:000001350 forkhead box protein P3 UniProtKB:Q9BZS1 UniProtKB:Q99JB6 HGNC:6106 FOXP3 CL:0000919 CD8-positive, CD25-positive, alpha-beta regulatory T cell RO:0002104 has plasma membrane part positive True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0000919 CD8-positive, CD25-positive, alpha-beta regulatory T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000919 CD8-positive, CD25-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000919 CD8-positive, CD25-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000920 CD8-positive, CD28-negative, alpha-beta regulatory T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000920 CD8-positive, CD28-negative, alpha-beta regulatory T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001841 T-cell-specific surface glycoprotein CD28 CD28 (label) UniProtKB:P10747 UniProtKB:P31041 IUPHARobj:2863 HGNC:1653 CD28 CL:0000920 CD8-positive, CD28-negative, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0000920 CD8-positive, CD28-negative, alpha-beta regulatory T cell BFO:0000051 has part positive True PR:000001350 forkhead box protein P3 UniProtKB:Q9BZS1 UniProtKB:Q99JB6 HGNC:6106 FOXP3 CL:0000920 CD8-positive, CD28-negative, alpha-beta regulatory T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0000920 CD8-positive, CD28-negative, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000920 CD8-positive, CD28-negative, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000921 type I NK T cell RO:0002104 has plasma membrane part positive False PR:000001874 KLRB1-like protein PIRSF:PIRSF038804 CL:0000922 type II NK T cell RO:0002104 has plasma membrane part positive False PR:000001874 KLRB1-like protein PIRSF:PIRSF038804 CL:0000923 CD4-positive type I NK T cell RO:0002104 has plasma membrane part positive True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 @@ -1035,7 +1035,7 @@ CL:0000934 CD4-positive, alpha-beta cytotoxic T cell CL:4030046 lacks_plasma_mem CL:0000934 CD4-positive, alpha-beta cytotoxic T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000935 CD4-negative, CD8-negative, alpha-beta intraepithelial T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000935 CD4-negative, CD8-negative, alpha-beta intraepithelial T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A -CL:0000935 CD4-negative, CD8-negative, alpha-beta intraepithelial T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0000935 CD4-negative, CD8-negative, alpha-beta intraepithelial T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0000936 early lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0000936 early lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0000936 early lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM @@ -1081,7 +1081,7 @@ CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_p CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0000941 thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -1092,7 +1092,7 @@ CL:0000942 thymic plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_p CL:0000942 thymic plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0000942 thymic plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000942 thymic plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000942 thymic plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0000942 thymic plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0000942 thymic plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) UniProtKB:P26951 UniProtKB:P26952 IUPHARobj:1705 HGNC:6012 IL3RA CL:0000943 Be1 Cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0000943 Be1 Cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -1204,7 +1204,7 @@ CL:0000961 Bm1 B cell CL:4030046 lacks_plasma_membrane_part negative True PR:000 CL:0000961 Bm1 B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000002037 complement component C1q receptor CD93 (exact); CDw93 (exact) UniProtKB:Q9NPY3 UniProtKB:O89103 HGNC:15855 CD93 CL:0000961 Bm1 B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0000961 Bm1 B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000961 Bm1 B cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000961 Bm1 B cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000961 Bm1 B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000961 Bm1 B cell RO:0002104 has plasma membrane part positive False PR:000001338 complement receptor type 2 CD21 (exact) UniProtKB:P20023 UniProtKB:P19070 PIRSF:PIRSF002484 HGNC:2336 CR2 CL:0000962 Bm2 B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E @@ -1213,7 +1213,7 @@ CL:0000962 Bm2 B cell CL:4030046 lacks_plasma_membrane_part negative False PR:00 CL:0000962 Bm2 B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000002037 complement component C1q receptor CD93 (exact); CDw93 (exact) UniProtKB:Q9NPY3 UniProtKB:O89103 HGNC:15855 CD93 CL:0000962 Bm2 B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0000962 Bm2 B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000962 Bm2 B cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000962 Bm2 B cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000962 Bm2 B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000962 Bm2 B cell RO:0002104 has plasma membrane part positive False PR:000001338 complement receptor type 2 CD21 (exact) UniProtKB:P20023 UniProtKB:P19070 PIRSF:PIRSF002484 HGNC:2336 CR2 CL:0000962 Bm2 B cell RO:0002104 has plasma membrane part positive True PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 @@ -1337,7 +1337,7 @@ CL:0000989 CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasma_membran CL:0000989 CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0000989 CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000989 CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000989 CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000989 CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000989 CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000002978 lymphocyte antigen 6G UniProtKB:P35461 CL:0000990 conventional dendritic cell RO:0015015 has high plasma membrane amount high True PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) UniProtKB:P20702 UniProtKB:Q9QXH4 IUPHARobj:2454 HGNC:6152 ITGAX CL:0000990 conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -1352,7 +1352,7 @@ CL:0000991 CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_plasma_me CL:0000991 CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0000991 CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000991 CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000991 CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000991 CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000991 CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001292 C-type lectin domain family 4 member C CD303 (exact) UniProtKB:Q8WTT0 HGNC:13258 CLEC4C CL:0000991 CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001398 leukocyte immunoglobulin-like receptor subfamily A member 4 CD85 (exact); CD85g (exact) UniProtKB:P59901 IUPHARobj:2896 HGNC:15503 LILRA4 CL:0000991 CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) UniProtKB:P26951 UniProtKB:P26952 IUPHARobj:1705 HGNC:6012 IL3RA @@ -1366,7 +1366,7 @@ CL:0000992 immature CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasm CL:0000992 immature CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0000992 immature CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000992 immature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000992 immature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000992 immature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000992 immature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000002978 lymphocyte antigen 6G UniProtKB:P35461 CL:0000993 mature CD11c-low plasmacytoid dendritic cell RO:0015015 has high plasma membrane amount high True PR:000001412 CD86 molecule CD28LG2 (related); CD86 (label) UniProtKB:P42081 UniProtKB:P42082 IUPHARobj:2745 HGNC:1705 CD86 CL:0000993 mature CD11c-low plasmacytoid dendritic cell RO:0015015 has high plasma membrane amount high True PR:000001438 CD80 molecule CD28LG (related); CD28LG1 (related); CD80 (label) UniProtKB:P33681 UniProtKB:Q00609 IUPHARobj:2744 HGNC:1700 CD80 @@ -1378,7 +1378,7 @@ CL:0000993 mature CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasma_ CL:0000993 mature CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0000993 mature CD11c-low plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000993 mature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000993 mature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000993 mature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000993 mature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001310 CD83 molecule CD83 (label) UniProtKB:Q01151 UniProtKB:O88324 HGNC:1703 CD83 CL:0000993 mature CD11c-low plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000002978 lymphocyte antigen 6G UniProtKB:P35461 CL:0000994 immature CD11c-negative plasmacytoid dendritic cell RO:0015016 has low plasma membrane amount low True PR:000001412 CD86 molecule CD28LG2 (related); CD86 (label) UniProtKB:P42081 UniProtKB:P42082 IUPHARobj:2745 HGNC:1705 CD86 @@ -1390,7 +1390,7 @@ CL:0000994 immature CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_ CL:0000994 immature CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000994 immature CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001438 CD80 molecule CD28LG (related); CD28LG1 (related); CD80 (label) UniProtKB:P33681 UniProtKB:Q00609 IUPHARobj:2744 HGNC:1700 CD80 CL:0000994 immature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000994 immature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000994 immature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000994 immature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001292 C-type lectin domain family 4 member C CD303 (exact) UniProtKB:Q8WTT0 HGNC:13258 CLEC4C CL:0000994 immature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001398 leukocyte immunoglobulin-like receptor subfamily A member 4 CD85 (exact); CD85g (exact) UniProtKB:P59901 IUPHARobj:2896 HGNC:15503 LILRA4 CL:0000994 immature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) UniProtKB:P26951 UniProtKB:P26952 IUPHARobj:1705 HGNC:6012 IL3RA @@ -1417,7 +1417,7 @@ CL:0000996 mature CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_pl CL:0000996 mature CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0000996 mature CD11c-negative plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0000996 mature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0000996 mature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0000996 mature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0000996 mature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001292 C-type lectin domain family 4 member C CD303 (exact) UniProtKB:Q8WTT0 HGNC:13258 CLEC4C CL:0000996 mature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001310 CD83 molecule CD83 (label) UniProtKB:Q01151 UniProtKB:O88324 HGNC:1703 CD83 CL:0000996 mature CD11c-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001398 leukocyte immunoglobulin-like receptor subfamily A member 4 CD85 (exact); CD85g (exact) UniProtKB:P59901 IUPHARobj:2896 HGNC:15503 LILRA4 @@ -1551,7 +1551,7 @@ CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0001008 Kit and Sca1-positive hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001083 CD2 molecule CD2 (label) UniProtKB:P06729 UniProtKB:P08920 IUPHARobj:2600; PIRSF:PIRSF001984 HGNC:1639 CD2 @@ -1710,7 +1710,7 @@ CL:0001021 CD34-positive, CD38-positive common lymphoid progenitor CL:4030046 la CL:0001021 CD34-positive, CD38-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000002981 lymphocyte antigen 76 (mouse) CL:0001021 CD34-positive, CD38-positive common lymphoid progenitor RO:0002104 has plasma membrane part positive False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0001021 CD34-positive, CD38-positive common lymphoid progenitor RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001021 CD34-positive, CD38-positive common lymphoid progenitor RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001021 CD34-positive, CD38-positive common lymphoid progenitor RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001021 CD34-positive, CD38-positive common lymphoid progenitor RO:0002104 has plasma membrane part positive False PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 CL:0001021 CD34-positive, CD38-positive common lymphoid progenitor RO:0002104 has plasma membrane part positive True PR:000001898 neprilysin CD10 (exact) UniProtKB:P08473 UniProtKB:Q61391 IUPHARobj:1611; PIRSF:PIRSF501074 HGNC:7154 MME CL:0001022 CD115-positive monocyte RO:0002104 has plasma membrane part positive True PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM @@ -1762,7 +1762,7 @@ CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lac CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0001025 Kit-positive, Sca1-positive common lymphoid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001083 CD2 molecule CD2 (label) UniProtKB:P06729 UniProtKB:P08920 IUPHARobj:2600; PIRSF:PIRSF001984 HGNC:1639 CD2 @@ -1781,7 +1781,7 @@ CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lac CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0001026 CD34-positive, CD38-positive common myeloid progenitor CL:4030046 lacks_plasma_membrane_part negative False PR:000001083 CD2 molecule CD2 (label) UniProtKB:P06729 UniProtKB:P08920 IUPHARobj:2600; PIRSF:PIRSF001984 HGNC:1639 CD2 @@ -1804,7 +1804,7 @@ CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membran CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001083 CD2 molecule CD2 (label) UniProtKB:P06729 UniProtKB:P08920 IUPHARobj:2600; PIRSF:PIRSF001984 HGNC:1639 CD2 @@ -1817,7 +1817,7 @@ CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membran CL:0001027 CD7-negative lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000002981 lymphocyte antigen 76 (mouse) CL:0001027 CD7-negative lymphoid progenitor cell RO:0002104 has plasma membrane part positive True PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0001028 CD7-positive lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001028 CD7-positive lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001028 CD7-positive lymphoid progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001028 CD7-positive lymphoid progenitor cell RO:0002104 has plasma membrane part positive True PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0001028 CD7-positive lymphoid progenitor cell RO:0002104 has plasma membrane part positive True PR:000001836 CD7 molecule CD7 (label) UniProtKB:P09564 UniProtKB:P50283 PIRSF:PIRSF038791 HGNC:1695 CD7 CL:0001029 common dendritic progenitor RO:0015016 has low plasma membrane amount low True PR:000002065 mast/stem cell growth factor receptor CD117 (exact) UniProtKB:P10721 UniProtKB:P05532 IUPHARobj:1805; PIRSF:PIRSF500951 HGNC:6342 KIT @@ -1852,7 +1852,7 @@ CL:0001041 CD8-positive, CXCR3-positive, alpha-beta regulatory T cell CL:4030046 CL:0001041 CD8-positive, CXCR3-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0001041 CD8-positive, CXCR3-positive, alpha-beta regulatory T cell RO:0002104 has plasma membrane part positive True PR:000001207 C-X-C chemokine receptor type 3 CD183 (exact) UniProtKB:P49682 UniProtKB:O88410 IUPHARobj:70; PIRSF:PIRSF501023 HGNC:4540 CXCR3 CL:0001041 CD8-positive, CXCR3-positive, alpha-beta regulatory T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0001041 CD8-positive, CXCR3-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0001041 CD8-positive, CXCR3-positive, alpha-beta regulatory T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0001042 T-helper 22 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0001042 T-helper 22 cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001043 activated CD4-positive, alpha-beta T cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001318 L-selectin CD62 (exact); CD62L (exact) UniProtKB:P14151 UniProtKB:P18337 PIRSF:PIRSF002421 HGNC:10720 SELL @@ -1867,16 +1867,16 @@ CL:0001044 effector CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_memb CL:0001044 effector CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0001044 effector CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001044 effector CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001044 effector CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001044 effector CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001045 naive CCR4-positive regulatory T cell RO:0015015 has high plasma membrane amount high False PR:000001318 L-selectin CD62 (exact); CD62L (exact) UniProtKB:P14151 UniProtKB:P18337 PIRSF:PIRSF002421 HGNC:10720 SELL CL:0001045 naive CCR4-positive regulatory T cell RO:0015016 has low plasma membrane amount low False PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) UniProtKB:P16070 UniProtKB:P15379 HGNC:1681 CD44 CL:0001045 naive CCR4-positive regulatory T cell RO:0015016 has low plasma membrane amount low False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0001045 naive CCR4-positive regulatory T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001045 naive CCR4-positive regulatory T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0001045 naive CCR4-positive regulatory T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0001045 naive CCR4-positive regulatory T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0001045 naive CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001045 naive CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001045 naive CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001045 naive CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001045 naive CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001200 C-C chemokine receptor type 4 CD194 (exact) UniProtKB:P51679 UniProtKB:P51680 IUPHARobj:61 HGNC:1605 CCR4 CL:0001045 naive CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0001045 naive CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA @@ -1884,7 +1884,7 @@ CL:0001046 memory CCR4-positive regulatory T cell RO:0015016 has low plasma memb CL:0001046 memory CCR4-positive regulatory T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0001046 memory CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001046 memory CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001046 memory CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0001046 memory CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0001046 memory CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001200 C-C chemokine receptor type 4 CD194 (exact) UniProtKB:P51679 UniProtKB:P51680 IUPHARobj:61 HGNC:1605 CCR4 CL:0001046 memory CCR4-positive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0001047 CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T cell RO:0015016 has low plasma membrane amount low False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R @@ -1908,14 +1908,14 @@ CL:0001049 activated CD8-positive, alpha-beta T cell, human RO:0002104 has plasm CL:0001049 activated CD8-positive, alpha-beta T cell, human RO:0002104 has plasma membrane part positive True PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 CL:0001049 activated CD8-positive, alpha-beta T cell, human RO:0002104 has plasma membrane part positive True PR:000002015 MHC class II histocompatibility antigen alpha chain DRA UniProtKB:P01903 HGNC:4947 HLA-DRA CL:0001049 activated CD8-positive, alpha-beta T cell, human RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0001049 activated CD8-positive, alpha-beta T cell, human BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0001049 activated CD8-positive, alpha-beta T cell, human BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0001050 effector CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001050 effector CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0001050 effector CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001050 effector CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001050 effector CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001050 effector CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0001050 effector CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0001050 effector CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0001050 effector CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0001051 CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001202 C-C chemokine receptor type 6 CD196 (exact) UniProtKB:P51684 UniProtKB:O54689 IUPHARobj:63 HGNC:1607 CCR6 CL:0001051 CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001207 C-X-C chemokine receptor type 3 CD183 (exact) UniProtKB:P49682 UniProtKB:O88410 IUPHARobj:70; PIRSF:PIRSF501023 HGNC:4540 CXCR3 CL:0001051 CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) @@ -1925,7 +1925,7 @@ CL:0001052 CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell CL:403 CL:0001052 CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001207 C-X-C chemokine receptor type 3 CD183 (exact) UniProtKB:P49682 UniProtKB:O88410 IUPHARobj:70; PIRSF:PIRSF501023 HGNC:4540 CXCR3 CL:0001052 CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0001052 CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0001052 CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0001052 CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0001053 IgD-negative memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001053 IgD-negative memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001935 syndecan-1 CD138 (exact) UniProtKB:P18827 UniProtKB:P18828 PIRSF:PIRSF015854 HGNC:10658 SDC1 CL:0001053 IgD-negative memory B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -1983,13 +1983,13 @@ CL:0001060 hematopoietic oligopotent progenitor cell, lineage-negative CL:403004 CL:0001060 hematopoietic oligopotent progenitor cell, lineage-negative CL:4030046 lacks_plasma_membrane_part negative True PR:000002981 lymphocyte antigen 76 (mouse) CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0001065 innate lymphoid cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001065 innate lymphoid cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001066 erythroid progenitor cell, mammalian CL:4030046 lacks_plasma_membrane_part negative True PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -2016,65 +2016,65 @@ CL:0001071 group 3 innate lymphoid cell BFO:0000051 has part positive True PR:00 CL:0001072 CD34-negative, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001072 CD34-negative, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0001072 CD34-negative, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E -CL:0001072 CD34-negative, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative True PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 +CL:0001072 CD34-negative, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative True PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 HGNC:1662 CD34 CL:0001072 CD34-negative, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000002065 mast/stem cell growth factor receptor CD117 (exact) UniProtKB:P10721 UniProtKB:P05532 IUPHARobj:1805; PIRSF:PIRSF500951 HGNC:6342 KIT -CL:0001072 CD34-negative, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 +CL:0001072 CD34-negative, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 HGNC:6342 KIT CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E -CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 +CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 HGNC:1662 CD34 CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000002065 mast/stem cell growth factor receptor CD117 (exact) UniProtKB:P10721 UniProtKB:P05532 IUPHARobj:1805; PIRSF:PIRSF500951 HGNC:6342 KIT -CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 -CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) UniProtKB:P13591-1; UniProtKB:P13591-2; UniProtKB:P13591-3; UniProtKB:P13591-4; UniProtKB:P13591-5; UniProtKB:P13591-6; UniProtKB:P13591 UniProtKB:P13591 +CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 HGNC:6342 KIT +CL:0001073 CD34-negative, CD56-positive, CD117-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) UniProtKB:P13591-1; UniProtKB:P13591-2; UniProtKB:P13591-3; UniProtKB:P13591-4; UniProtKB:P13591-5; UniProtKB:P13591-6; UniProtKB:P13591 UniProtKB:P13591 HGNC:7656 NCAM1 CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive False PR:000002065 mast/stem cell growth factor receptor CD117 (exact) UniProtKB:P10721 UniProtKB:P05532 IUPHARobj:1805; PIRSF:PIRSF500951 HGNC:6342 KIT -CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive True PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 -CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive True PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) UniProtKB:P13591-1; UniProtKB:P13591-2; UniProtKB:P13591-3; UniProtKB:P13591-4; UniProtKB:P13591-5; UniProtKB:P13591-6; UniProtKB:P13591 UniProtKB:P13591 -CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive True PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 +CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive True PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 HGNC:6342 KIT +CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive True PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) UniProtKB:P13591-1; UniProtKB:P13591-2; UniProtKB:P13591-3; UniProtKB:P13591-4; UniProtKB:P13591-5; UniProtKB:P13591-6; UniProtKB:P13591 UniProtKB:P13591 HGNC:7656 NCAM1 +CL:0001074 CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human RO:0002104 has plasma membrane part positive True PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 HGNC:1662 CD34 CL:0001075 KLRG1-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001075 KLRG1-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0001075 KLRG1-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E -CL:0001075 KLRG1-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 +CL:0001075 KLRG1-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 HGNC:1662 CD34 CL:0001075 KLRG1-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000002065 mast/stem cell growth factor receptor CD117 (exact) UniProtKB:P10721 UniProtKB:P05532 IUPHARobj:1805; PIRSF:PIRSF500951 HGNC:6342 KIT -CL:0001075 KLRG1-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 -CL:0001075 KLRG1-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:Q96E93 killer cell lectin-like receptor subfamily G member 1 (human) UniProtKB:Q96E93-1; UniProtKB:Q96E93-2; UniProtKB:Q96E93 Reactome:R-HSA-198006; UniProtKB:Q96E93 +CL:0001075 KLRG1-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 HGNC:6342 KIT +CL:0001075 KLRG1-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:Q96E93 killer cell lectin-like receptor subfamily G member 1 (human) UniProtKB:Q96E93-1; UniProtKB:Q96E93-2; UniProtKB:Q96E93 Reactome:R-HSA-198006; UniProtKB:Q96E93 HGNC:6380 KLRG1 CL:0001076 NKp46-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001076 NKp46-positive innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001893 natural cytotoxicity triggering receptor 1 CD335 (exact) UniProtKB:O76036 UniProtKB:Q8C567 HGNC:6731 NCR1 CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000002065 mast/stem cell growth factor receptor CD117 (exact) UniProtKB:P10721 UniProtKB:P05532 IUPHARobj:1805; PIRSF:PIRSF500951 HGNC:6342 KIT -CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:O76036 natural cytotoxicity triggering receptor 1 (human) CD335 (exact) UniProtKB:O76036-1; UniProtKB:O76036-2; UniProtKB:O76036-3; UniProtKB:O76036-4; UniProtKB:O76036-5; UniProtKB:O76036-6; UniProtKB:O76036 UniProtKB:O76036 -CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 -CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) UniProtKB:P13591-1; UniProtKB:P13591-2; UniProtKB:P13591-3; UniProtKB:P13591-4; UniProtKB:P13591-5; UniProtKB:P13591-6; UniProtKB:P13591 UniProtKB:P13591 -CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 +CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:O76036 natural cytotoxicity triggering receptor 1 (human) CD335 (exact) UniProtKB:O76036-1; UniProtKB:O76036-2; UniProtKB:O76036-3; UniProtKB:O76036-4; UniProtKB:O76036-5; UniProtKB:O76036-6; UniProtKB:O76036 UniProtKB:O76036 HGNC:6731 NCR1 +CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P10721 mast/stem cell growth factor receptor Kit (human) CD117 (exact) UniProtKB:P10721-1; UniProtKB:P10721-2; UniProtKB:P10721-4; UniProtKB:P10721 DTO:03100231; UniProtKB:P10721 HGNC:6342 KIT +CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) UniProtKB:P13591-1; UniProtKB:P13591-2; UniProtKB:P13591-3; UniProtKB:P13591-4; UniProtKB:P13591-5; UniProtKB:P13591-6; UniProtKB:P13591 UniProtKB:P13591 HGNC:7656 NCAM1 +CL:0001076 NKp46-positive innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P28906 hematopoietic progenitor cell antigen CD34 (human) CD34 (label) UniProtKB:P28906-1; UniProtKB:P28906-2; UniProtKB:P28906 UniProtKB:P28906 HGNC:1662 CD34 CL:0001077 ILC1, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001077 ILC1, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001077 ILC1, human BFO:0000051 has part positive False PR:000001835 T-box transcription factor TBX21 UniProtKB:Q9UL17 UniProtKB:Q9JKD8 HGNC:11599 TBX21 CL:0001077 ILC1, human RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R -CL:0001077 ILC1, human RO:0002104 has plasma membrane part positive True PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 +CL:0001077 ILC1, human RO:0002104 has plasma membrane part positive True PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 HGNC:6024 IL7R CL:0001077 ILC1, human BFO:0000051 has part positive True PR:Q9UL17 T-box transcription factor TBX21 (human) UniProtKB:Q9UL17 UniProtKB:Q9UL17 HGNC:11599 TBX21 CL:0001078 group 3 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001078 group 3 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001078 group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0001078 group 3 innate lymphoid cell, human BFO:0000051 has part positive False PR:000003455 nuclear receptor ROR-gamma isoform 2 UniProtKB:P51450-2 -CL:0001078 group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 +CL:0001078 group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 HGNC:6024 IL7R CL:0001079 NKp44-positive group 3 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001079 NKp44-positive group 3 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001079 NKp44-positive group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0001079 NKp44-positive group 3 innate lymphoid cell, human BFO:0000051 has part positive False PR:000003455 nuclear receptor ROR-gamma isoform 2 UniProtKB:P51450-2 -CL:0001079 NKp44-positive group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:O95944 natural cytotoxicity triggering receptor 2 (human) CD336 (exact) UniProtKB:O95944-1; UniProtKB:O95944-2; UniProtKB:O95944-3; UniProtKB:O95944 UniProtKB:O95944 -CL:0001079 NKp44-positive group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 +CL:0001079 NKp44-positive group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:O95944 natural cytotoxicity triggering receptor 2 (human) CD336 (exact) UniProtKB:O95944-1; UniProtKB:O95944-2; UniProtKB:O95944-3; UniProtKB:O95944 UniProtKB:O95944 HGNC:6732 NCR2 +CL:0001079 NKp44-positive group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 HGNC:6024 IL7R CL:0001080 NKp44-negative group 3 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001080 NKp44-negative group 3 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E -CL:0001080 NKp44-negative group 3 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative True PR:O95944 natural cytotoxicity triggering receptor 2 (human) CD336 (exact) UniProtKB:O95944-1; UniProtKB:O95944-2; UniProtKB:O95944-3; UniProtKB:O95944 UniProtKB:O95944 +CL:0001080 NKp44-negative group 3 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative True PR:O95944 natural cytotoxicity triggering receptor 2 (human) CD336 (exact) UniProtKB:O95944-1; UniProtKB:O95944-2; UniProtKB:O95944-3; UniProtKB:O95944 UniProtKB:O95944 HGNC:6732 NCR2 CL:0001080 NKp44-negative group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0001080 NKp44-negative group 3 innate lymphoid cell, human BFO:0000051 has part positive False PR:000003455 nuclear receptor ROR-gamma isoform 2 UniProtKB:P51450-2 -CL:0001080 NKp44-negative group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 +CL:0001080 NKp44-negative group 3 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 HGNC:6024 IL7R CL:0001081 group 2 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001081 group 2 innate lymphoid cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001081 group 2 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA @@ -2082,19 +2082,19 @@ CL:0001081 group 2 innate lymphoid cell, human RO:0002104 has plasma membrane pa CL:0001081 group 2 innate lymphoid cell, human RO:0002104 has plasma membrane part positive False PR:000001874 KLRB1-like protein PIRSF:PIRSF038804 CL:0001081 group 2 innate lymphoid cell, human BFO:0000051 has part positive False PR:000001941 trans-acting T-cell-specific transcription factor GATA-3 UniProtKB:P23771 UniProtKB:P23772 HGNC:4172 GATA3 CL:0001081 group 2 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P01589 interleukin-2 receptor subunit alpha (human) CD25 (exact) UniProtKB:P01589 UniProtKB:P01589 HGNC:6008 IL2RA -CL:0001081 group 2 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 -CL:0001081 group 2 innate lymphoid cell, human BFO:0000051 has part positive True PR:P23771 trans-acting T-cell-specific transcription factor GATA-3 (human) UniProtKB:P23771-1; UniProtKB:P23771-2; UniProtKB:P23771 Reactome:R-HSA-996768; UniProtKB:P23771 +CL:0001081 group 2 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:P16871 interleukin-7 receptor subunit alpha (human) CD127 (exact); CDw127 (exact) UniProtKB:P16871-1; UniProtKB:P16871-2; UniProtKB:P16871-3; UniProtKB:P16871-4; UniProtKB:P16871 UniProtKB:P16871 HGNC:6024 IL7R +CL:0001081 group 2 innate lymphoid cell, human BFO:0000051 has part positive True PR:P23771 trans-acting T-cell-specific transcription factor GATA-3 (human) UniProtKB:P23771-1; UniProtKB:P23771-2; UniProtKB:P23771 Reactome:R-HSA-996768; UniProtKB:P23771 HGNC:4172 GATA3 CL:0001081 group 2 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:Q12918 killer cell lectin-like receptor subfamily B member 1 (human) CD161 (exact) UniProtKB:Q12918 Reactome:R-HSA-2132225; UniProtKB:Q12918 HGNC:6373 KLRB1 CL:0001081 group 2 innate lymphoid cell, human RO:0002104 has plasma membrane part positive True PR:Q9Y5Y4 prostaglandin D2 receptor 2 (human) CD294 (exact) UniProtKB:Q9Y5Y4 DTO:02100741; Reactome:R-HSA-416895; UniProtKB:Q9Y5Y4 HGNC:4502 PTGDR2 CL:0001082 immature innate lymphoid cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001082 immature innate lymphoid cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative True PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0001200 lymphocyte of B lineage, CD19-positive CL:4030046 lacks_plasma_membrane_part negative True PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0001200 lymphocyte of B lineage, CD19-positive RO:0002104 has plasma membrane part positive True PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0001201 B cell, CD19-positive CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E @@ -2109,16 +2109,16 @@ CL:0001202 CD86-positive plasmablast RO:0002104 has plasma membrane part positiv CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive CL:4030046 lacks_plasma_membrane_part negative True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive True PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0001203 CD8-positive, alpha-beta memory T cell, CD45RO-positive BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0001204 CD4-positive, alpha-beta memory T cell, CD45RO-positive CL:4030046 lacks_plasma_membrane_part negative True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0001204 CD4-positive, alpha-beta memory T cell, CD45RO-positive CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0001204 CD4-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0001204 CD4-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0001204 CD4-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 +CL:0001204 CD4-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive True PR:000001017 receptor-type tyrosine-protein phosphatase C isoform CD45RO CD45RO (label) UniProtKB:P08575-4 HGNC:9666 PTPRC CL:0001204 CD4-positive, alpha-beta memory T cell, CD45RO-positive RO:0002104 has plasma membrane part positive True PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0002000 Kit-positive erythroid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002000 Kit-positive erythroid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 @@ -2211,7 +2211,7 @@ CL:0002004 CD34-negative, GlyA-negative proerythroblast CL:4030046 lacks_plasma_ CL:0002004 CD34-negative, GlyA-negative proerythroblast CL:4030046 lacks_plasma_membrane_part negative False PR:000002978 lymphocyte antigen 6G UniProtKB:P35461 CL:0002004 CD34-negative, GlyA-negative proerythroblast RO:0002104 has plasma membrane part positive False PR:000001945 transferrin receptor protein 1 CD71 (exact) UniProtKB:P02786 UniProtKB:Q62351 HGNC:11763 TFRC CL:0002005 CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002005 CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0002005 CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0002005 CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) UniProtKB:P26951 UniProtKB:P26952 IUPHARobj:1705 HGNC:6012 IL3RA CL:0002005 CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell RO:0002104 has plasma membrane part positive True PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0002005 CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell RO:0002104 has plasma membrane part positive True PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 @@ -2256,7 +2256,7 @@ CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell CL:4030046 la CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000002981 lymphocyte antigen 76 (mouse) CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell RO:0002104 has plasma membrane part positive False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell RO:0002104 has plasma membrane part positive False PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell RO:0002104 has plasma membrane part positive False PR:000001865 interleukin-3 receptor class 2 alpha chain CD123 (exact) UniProtKB:P26951 UniProtKB:P26952 IUPHARobj:1705 HGNC:6012 IL3RA CL:0002008 CD34-positive, CD38-positive eosinophil progenitor cell RO:0002104 has plasma membrane part positive False PR:000001867 interleukin-5 receptor subunit alpha CD125 (exact); CDw125 (exact) UniProtKB:Q01344 UniProtKB:P21183 IUPHARobj:1706; PIRSF:PIRSF018419 HGNC:6017 IL5RA @@ -2525,7 +2525,7 @@ CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_p CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0002033 short term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001083 CD2 molecule CD2 (label) UniProtKB:P06729 UniProtKB:P08920 IUPHARobj:2600; PIRSF:PIRSF001984 HGNC:1639 CD2 @@ -2551,7 +2551,7 @@ CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_pa CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0002034 long term hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001083 CD2 molecule CD2 (label) UniProtKB:P06729 UniProtKB:P08920 IUPHARobj:2600; PIRSF:PIRSF001984 HGNC:1639 CD2 @@ -2624,7 +2624,7 @@ CL:0002039 immature NK T cell stage I, mouse CL:4030046 lacks_plasma_membrane_pa CL:0002039 immature NK T cell stage I, mouse CL:4030046 lacks_plasma_membrane_part negative True PR:000001874 KLRB1-like protein PIRSF:PIRSF038804 CL:0002039 immature NK T cell stage I, mouse BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002039 immature NK T cell stage I, mouse BFO:0000051 has part positive False PR:000003469 early growth response protein 2 UniProtKB:P11161 UniProtKB:P08152 HGNC:3239 EGR2 -CL:0002039 immature NK T cell stage I, mouse BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002039 immature NK T cell stage I, mouse BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002040 immature NK T cell stage II, mouse RO:0015016 has low plasma membrane amount low True PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) UniProtKB:P25063 UniProtKB:P24807 HGNC:1645 CD24 CL:0002040 immature NK T cell stage II, mouse CL:4030046 lacks_plasma_membrane_part negative True PR:000001307 CD44 molecule CD44 (label); CDw44 (exact) UniProtKB:P16070 UniProtKB:P15379 HGNC:1681 CD44 CL:0002040 immature NK T cell stage II, mouse CL:4030046 lacks_plasma_membrane_part negative True PR:000001874 KLRB1-like protein PIRSF:PIRSF038804 @@ -2643,7 +2643,7 @@ CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 l CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0002043 CD34-positive, CD38-negative multipotent progenitor cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001083 CD2 molecule CD2 (label) UniProtKB:P06729 UniProtKB:P08920 IUPHARobj:2600; PIRSF:PIRSF001984 HGNC:1639 CD2 @@ -2672,7 +2672,7 @@ CL:0002045 fraction A pre-pro B cell RO:0015016 has low plasma membrane amount l CL:0002045 fraction A pre-pro B cell CL:4030046 lacks_plasma_membrane_part negative True PR:000002039 glutamyl aminopeptidase CD249 (exact) UniProtKB:Q07075 UniProtKB:P16406 IUPHARobj:1568 HGNC:3355 ENPEP CL:0002045 fraction A pre-pro B cell CL:4030046 lacks_plasma_membrane_part negative True PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002045 fraction A pre-pro B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002045 fraction A pre-pro B cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0002045 fraction A pre-pro B cell RO:0002104 has plasma membrane part positive True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0002045 fraction A pre-pro B cell RO:0002104 has plasma membrane part positive True PR:000001879 leukosialin CD43 (related) UniProtKB:P16150 UniProtKB:P15702 PIRSF:PIRSF001994 HGNC:11249 SPN CL:0002045 fraction A pre-pro B cell BFO:0000051 has part positive False PR:000001903 paired box protein PAX-5 UniProtKB:Q02548 UniProtKB:Q02650 HGNC:8619 PAX5 CL:0002045 fraction A pre-pro B cell RO:0002104 has plasma membrane part positive True PR:000002037 complement component C1q receptor CD93 (exact); CDw93 (exact) UniProtKB:Q9NPY3 UniProtKB:O89103 HGNC:15855 CD93 @@ -2691,7 +2691,7 @@ CL:0002047 fraction B precursor B cell CL:4030046 lacks_plasma_membrane_part neg CL:0002047 fraction B precursor B cell CL:4030046 lacks_plasma_membrane_part negative True PR:000002039 glutamyl aminopeptidase CD249 (exact) UniProtKB:Q07075 UniProtKB:P16406 IUPHARobj:1568 HGNC:3355 ENPEP CL:0002047 fraction B precursor B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002047 fraction B precursor B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002047 fraction B precursor B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002047 fraction B precursor B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002047 fraction B precursor B cell RO:0002104 has plasma membrane part positive False PR:000001879 leukosialin CD43 (related) UniProtKB:P16150 UniProtKB:P15702 PIRSF:PIRSF001994 HGNC:11249 SPN CL:0002047 fraction B precursor B cell RO:0002104 has plasma membrane part positive False PR:000001898 neprilysin CD10 (exact) UniProtKB:P08473 UniProtKB:Q61391 IUPHARobj:1611; PIRSF:PIRSF501074 HGNC:7154 MME CL:0002047 fraction B precursor B cell RO:0002104 has plasma membrane part positive False PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) UniProtKB:P25063 UniProtKB:P24807 HGNC:1645 CD24 @@ -2705,7 +2705,7 @@ CL:0002048 late pro-B cell RO:0002104 has plasma membrane part positive False PR CL:0002049 fraction C precursor B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002049 fraction C precursor B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002049 fraction C precursor B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002049 fraction C precursor B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002049 fraction C precursor B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002049 fraction C precursor B cell BFO:0000051 has part positive True PR:000001858 immunoglobulin iota chain CD179 (exact); CD179a (exact) UniProtKB:P12018 PIRSF:PIRSF038787 HGNC:12709 VPREB1 CL:0002049 fraction C precursor B cell BFO:0000051 has part positive True PR:000001859 immunoglobulin lambda-like polypeptide 1 CD179 (exact); CD179b (exact) UniProtKB:P15814 HGNC:5870 IGLL1 CL:0002049 fraction C precursor B cell RO:0002104 has plasma membrane part positive False PR:000001879 leukosialin CD43 (related) UniProtKB:P16150 UniProtKB:P15702 PIRSF:PIRSF001994 HGNC:11249 SPN @@ -2719,7 +2719,7 @@ CL:0002050 fraction C' precursor B cell RO:0015015 has high plasma membrane amou CL:0002050 fraction C' precursor B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002050 fraction C' precursor B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002050 fraction C' precursor B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002050 fraction C' precursor B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002050 fraction C' precursor B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002050 fraction C' precursor B cell RO:0002104 has plasma membrane part positive True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0002050 fraction C' precursor B cell RO:0002104 has plasma membrane part positive True PR:000001879 leukosialin CD43 (related) UniProtKB:P16150 UniProtKB:P15702 PIRSF:PIRSF001994 HGNC:11249 SPN CL:0002050 fraction C' precursor B cell RO:0002104 has plasma membrane part positive False PR:000001898 neprilysin CD10 (exact) UniProtKB:P08473 UniProtKB:Q61391 IUPHARobj:1611; PIRSF:PIRSF501074 HGNC:7154 MME @@ -2739,7 +2739,7 @@ CL:0002052 fraction D precursor B cell RO:0015016 has low plasma membrane amount CL:0002052 fraction D precursor B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002052 fraction D precursor B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002052 fraction D precursor B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002052 fraction D precursor B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002052 fraction D precursor B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002052 fraction D precursor B cell RO:0002104 has plasma membrane part positive True PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0002052 fraction D precursor B cell RO:0002104 has plasma membrane part positive False PR:000001898 neprilysin CD10 (exact) UniProtKB:P08473 UniProtKB:Q61391 IUPHARobj:1611; PIRSF:PIRSF501074 HGNC:7154 MME CL:0002052 fraction D precursor B cell RO:0002104 has plasma membrane part positive False PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) UniProtKB:P25063 UniProtKB:P24807 HGNC:1645 CD24 @@ -2775,7 +2775,7 @@ CL:0002056 fraction F mature B cell CL:4030046 lacks_plasma_membrane_part negati CL:0002056 fraction F mature B cell CL:4030046 lacks_plasma_membrane_part negative True PR:000002037 complement component C1q receptor CD93 (exact); CDw93 (exact) UniProtKB:Q9NPY3 UniProtKB:O89103 HGNC:15855 CD93 CL:0002056 fraction F mature B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002056 fraction F mature B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002056 fraction F mature B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002056 fraction F mature B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002056 fraction F mature B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002056 fraction F mature B cell RO:0002104 has plasma membrane part positive True PR:000001338 complement receptor type 2 CD21 (exact) UniProtKB:P20023 UniProtKB:P19070 PIRSF:PIRSF002484 HGNC:2336 CR2 CL:0002057 CD14-positive, CD16-negative classical monocyte RO:0015015 has high plasma membrane amount high False PR:000001199 C-C chemokine receptor type 2 CD192 (exact) UniProtKB:P41597 UniProtKB:P51683 IUPHARobj:59 HGNC:1603 CCR2 @@ -2791,7 +2791,7 @@ CL:0002058 Gr1-low non-classical monocyte RO:0015016 has low plasma membrane amo CL:0002058 Gr1-low non-classical monocyte RO:0015016 has low plasma membrane amount low True PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002058 Gr1-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002058 Gr1-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002058 Gr1-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002058 Gr1-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002058 Gr1-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002058 Gr1-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001199 C-C chemokine receptor type 2 CD192 (exact) UniProtKB:P41597 UniProtKB:P51683 IUPHARobj:59 HGNC:1603 CCR2 CL:0002058 Gr1-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -2803,7 +2803,7 @@ CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lack CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0002059 CD8-alpha-positive thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -2874,11 +2874,11 @@ CL:0002109 B220-positive CD38-positive naive B cell CL:4030046 lacks_plasma_memb CL:0002109 B220-positive CD38-positive naive B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001963 CD27 molecule CD27 (label); CD27L (exact) UniProtKB:P26842 UniProtKB:P41272 IUPHARobj:1876; PIRSF:PIRSF001966 HGNC:11922 CD27 CL:0002109 B220-positive CD38-positive naive B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002109 B220-positive CD38-positive naive B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002109 B220-positive CD38-positive naive B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002109 B220-positive CD38-positive naive B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002109 B220-positive CD38-positive naive B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002109 B220-positive CD38-positive naive B cell RO:0002104 has plasma membrane part positive False PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 CL:0002110 B220-low CD38-positive naive B cell RO:0015016 has low plasma membrane amount low False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002110 B220-low CD38-positive naive B cell RO:0015016 has low plasma membrane amount low True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002110 B220-low CD38-positive naive B cell RO:0015016 has low plasma membrane amount low True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002110 B220-low CD38-positive naive B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002110 B220-low CD38-positive naive B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001963 CD27 molecule CD27 (label); CD27L (exact) UniProtKB:P26842 UniProtKB:P41272 IUPHARobj:1876; PIRSF:PIRSF001966 HGNC:11922 CD27 CL:0002110 B220-low CD38-positive naive B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -2895,11 +2895,11 @@ CL:0002112 B220-positive CD38-negative unswitched memory B cell CL:4030046 lacks CL:0002112 B220-positive CD38-negative unswitched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001935 syndecan-1 CD138 (exact) UniProtKB:P18827 UniProtKB:P18828 PIRSF:PIRSF015854 HGNC:10658 SDC1 CL:0002112 B220-positive CD38-negative unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002112 B220-positive CD38-negative unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002112 B220-positive CD38-negative unswitched memory B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002112 B220-positive CD38-negative unswitched memory B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002112 B220-positive CD38-negative unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002112 B220-positive CD38-negative unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001963 CD27 molecule CD27 (label); CD27L (exact) UniProtKB:P26842 UniProtKB:P41272 IUPHARobj:1876; PIRSF:PIRSF001966 HGNC:11922 CD27 CL:0002113 B220-low CD38-negative unswitched memory B cell RO:0015016 has low plasma membrane amount low False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002113 B220-low CD38-negative unswitched memory B cell RO:0015016 has low plasma membrane amount low True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002113 B220-low CD38-negative unswitched memory B cell RO:0015016 has low plasma membrane amount low True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002113 B220-low CD38-negative unswitched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002113 B220-low CD38-negative unswitched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 CL:0002113 B220-low CD38-negative unswitched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001935 syndecan-1 CD138 (exact) UniProtKB:P18827 UniProtKB:P18828 PIRSF:PIRSF015854 HGNC:10658 SDC1 @@ -2916,12 +2916,12 @@ CL:0002115 B220-positive CD38-positive unswitched memory B cell CL:4030046 lacks CL:0002115 B220-positive CD38-positive unswitched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001935 syndecan-1 CD138 (exact) UniProtKB:P18827 UniProtKB:P18828 PIRSF:PIRSF015854 HGNC:10658 SDC1 CL:0002115 B220-positive CD38-positive unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002115 B220-positive CD38-positive unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002115 B220-positive CD38-positive unswitched memory B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002115 B220-positive CD38-positive unswitched memory B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002115 B220-positive CD38-positive unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002115 B220-positive CD38-positive unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 CL:0002115 B220-positive CD38-positive unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001963 CD27 molecule CD27 (label); CD27L (exact) UniProtKB:P26842 UniProtKB:P41272 IUPHARobj:1876; PIRSF:PIRSF001966 HGNC:11922 CD27 CL:0002116 B220-low CD38-positive unswitched memory B cell RO:0015016 has low plasma membrane amount low False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002116 B220-low CD38-positive unswitched memory B cell RO:0015016 has low plasma membrane amount low True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002116 B220-low CD38-positive unswitched memory B cell RO:0015016 has low plasma membrane amount low True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002116 B220-low CD38-positive unswitched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002116 B220-low CD38-positive unswitched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001935 syndecan-1 CD138 (exact) UniProtKB:P18827 UniProtKB:P18828 PIRSF:PIRSF015854 HGNC:10658 SDC1 CL:0002116 B220-low CD38-positive unswitched memory B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -2963,12 +2963,12 @@ CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001935 syndecan-1 CD138 (exact) UniProtKB:P18827 UniProtKB:P18828 PIRSF:PIRSF015854 HGNC:10658 SDC1 CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell RO:0002104 has plasma membrane part positive False PR:000001408 ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 CD38 (exact) UniProtKB:P28907 UniProtKB:P56528 IUPHARobj:2766 HGNC:1667 CD38 CL:0002122 B220-positive CD38-positive IgG-negative class switched memory B cell RO:0002104 has plasma membrane part positive False PR:000001963 CD27 molecule CD27 (label); CD27L (exact) UniProtKB:P26842 UniProtKB:P41272 IUPHARobj:1876; PIRSF:PIRSF001966 HGNC:11922 CD27 CL:0002123 B220-low CD38-positive IgG-negative class switched memory B cell RO:0015016 has low plasma membrane amount low False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002123 B220-low CD38-positive IgG-negative class switched memory B cell RO:0015016 has low plasma membrane amount low True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002123 B220-low CD38-positive IgG-negative class switched memory B cell RO:0015016 has low plasma membrane amount low True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002123 B220-low CD38-positive IgG-negative class switched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002123 B220-low CD38-positive IgG-negative class switched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001935 syndecan-1 CD138 (exact) UniProtKB:P18827 UniProtKB:P18828 PIRSF:PIRSF015854 HGNC:10658 SDC1 CL:0002123 B220-low CD38-positive IgG-negative class switched memory B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -2989,7 +2989,7 @@ CL:0002126 CD25-positive, CD27-positive immature gamma-delta T cell RO:0002104 h CL:0002128 Tc17 cell RO:0015015 has high plasma membrane amount high True PR:000001201 C-C chemokine receptor type 5 CD195 (exact) UniProtKB:P51681 UniProtKB:P51682 IUPHARobj:62 HGNC:1606 CCR5 CL:0002128 Tc17 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002128 Tc17 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002128 Tc17 cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0002128 Tc17 cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0002128 Tc17 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001318 L-selectin CD62 (exact); CD62L (exact) UniProtKB:P14151 UniProtKB:P18337 PIRSF:PIRSF002421 HGNC:10720 SELL CL:0002128 Tc17 cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R CL:0002128 Tc17 cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A @@ -2997,7 +2997,7 @@ CL:0002128 Tc17 cell RO:0002104 has plasma membrane part positive True PR:000001 CL:0002128 Tc17 cell RO:0002104 has plasma membrane part positive False PR:000001343 CD69 molecule CD69 (label) UniProtKB:Q07108 UniProtKB:P37217 HGNC:1694 CD69 CL:0002128 Tc17 cell RO:0002104 has plasma membrane part positive False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0002128 Tc17 cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0002128 Tc17 cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002128 Tc17 cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002151 late promyelocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM CL:0002151 late promyelocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001483 low affinity immunoglobulin gamma Fc region receptor III CD16 (exact) UniProtKB:P08508 CL:0002151 late promyelocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) UniProtKB:P25063 UniProtKB:P24807 HGNC:1645 CD24 @@ -3174,7 +3174,7 @@ CL:0002395 Gr1-high classical monocyte RO:0015015 has high plasma membrane amoun CL:0002395 Gr1-high classical monocyte RO:0015015 has high plasma membrane amount high True PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002395 Gr1-high classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002395 Gr1-high classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002395 Gr1-high classical monocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002395 Gr1-high classical monocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002395 Gr1-high classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002395 Gr1-high classical monocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001206 CX3C chemokine receptor 1 UniProtKB:P49238 UniProtKB:Q9Z0D9 IUPHARobj:74; PIRSF:PIRSF501025 HGNC:2558 CX3CR1 CL:0002395 Gr1-high classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3221,7 +3221,7 @@ CL:0002402 Peyer's patch B cell CL:4030046 lacks_plasma_membrane_part negative F CL:0002402 Peyer's patch B cell CL:4030046 lacks_plasma_membrane_part negative True PR:000002037 complement component C1q receptor CD93 (exact); CDw93 (exact) UniProtKB:Q9NPY3 UniProtKB:O89103 HGNC:15855 CD93 CL:0002402 Peyer's patch B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002402 Peyer's patch B cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002402 Peyer's patch B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002402 Peyer's patch B cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002402 Peyer's patch B cell RO:0002104 has plasma membrane part positive False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002402 Peyer's patch B cell RO:0002104 has plasma membrane part positive True PR:000001338 complement receptor type 2 CD21 (exact) UniProtKB:P20023 UniProtKB:P19070 PIRSF:PIRSF002484 HGNC:2336 CR2 CL:0002405 gamma-delta thymocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 @@ -3295,26 +3295,26 @@ CL:0002426 CD11b-positive, CD27-positive natural killer cell, mouse RO:0002104 h CL:0002427 resting double-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002427 resting double-positive thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002427 resting double-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0002427 resting double-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002427 resting double-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002428 double-positive blast RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002428 double-positive blast BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002428 double-positive blast RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0002428 double-positive blast BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002428 double-positive blast BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002429 CD69-positive double-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002429 CD69-positive double-positive thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002429 CD69-positive double-positive thymocyte RO:0002104 has plasma membrane part positive True PR:000001343 CD69 molecule CD69 (label) UniProtKB:Q07108 UniProtKB:P37217 HGNC:1694 CD69 CL:0002429 CD69-positive double-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0002429 CD69-positive double-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002429 CD69-positive double-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002430 CD4-intermediate, CD8-positive double-positive thymocyte RO:0015016 has low plasma membrane amount low True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002430 CD4-intermediate, CD8-positive double-positive thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002430 CD4-intermediate, CD8-positive double-positive thymocyte RO:0002104 has plasma membrane part positive True PR:000001343 CD69 molecule CD69 (label) UniProtKB:Q07108 UniProtKB:P37217 HGNC:1694 CD69 CL:0002430 CD4-intermediate, CD8-positive double-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0002430 CD4-intermediate, CD8-positive double-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002430 CD4-intermediate, CD8-positive double-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002431 CD4-positive, CD8-intermediate double-positive thymocyte RO:0015016 has low plasma membrane amount low True PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0002431 CD4-positive, CD8-intermediate double-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002431 CD4-positive, CD8-intermediate double-positive thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002431 CD4-positive, CD8-intermediate double-positive thymocyte RO:0002104 has plasma membrane part positive True PR:000001343 CD69 molecule CD69 (label) UniProtKB:Q07108 UniProtKB:P37217 HGNC:1694 CD69 -CL:0002431 CD4-positive, CD8-intermediate double-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002431 CD4-positive, CD8-intermediate double-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002432 CD24-positive, CD4 single-positive thymocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002432 CD24-positive, CD4 single-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002432 CD24-positive, CD4 single-positive thymocyte RO:0002104 has plasma membrane part positive True PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) UniProtKB:P25063 UniProtKB:P24807 HGNC:1645 CD24 @@ -3325,12 +3325,12 @@ CL:0002434 CD24-positive, CD8 single-positive thymocyte CL:4030046 lacks_plasma_ CL:0002434 CD24-positive, CD8 single-positive thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002434 CD24-positive, CD8 single-positive thymocyte RO:0002104 has plasma membrane part positive True PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) UniProtKB:P25063 UniProtKB:P24807 HGNC:1645 CD24 CL:0002434 CD24-positive, CD8 single-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0002434 CD24-positive, CD8 single-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002434 CD24-positive, CD8 single-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002435 CD69-positive, CD8-positive single-positive thymocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002435 CD69-positive, CD8-positive single-positive thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002435 CD69-positive, CD8-positive single-positive thymocyte RO:0002104 has plasma membrane part positive True PR:000001343 CD69 molecule CD69 (label) UniProtKB:Q07108 UniProtKB:P37217 HGNC:1694 CD69 CL:0002435 CD69-positive, CD8-positive single-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0002435 CD69-positive, CD8-positive single-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002435 CD69-positive, CD8-positive single-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002436 mature CD4 single-positive thymocyte RO:0015016 has low plasma membrane amount low True PR:000001932 signal transducer CD24 CD24 (label); CD24A (related) UniProtKB:P25063 UniProtKB:P24807 HGNC:1645 CD24 CL:0002436 mature CD4 single-positive thymocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0002436 mature CD4 single-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 @@ -3338,7 +3338,7 @@ CL:0002437 mature CD8 single-positive thymocyte RO:0015016 has low plasma membra CL:0002437 mature CD8 single-positive thymocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002437 mature CD8 single-positive thymocyte BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002437 mature CD8 single-positive thymocyte RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0002437 mature CD8 single-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0002437 mature CD8 single-positive thymocyte BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0002438 NK1.1-positive natural killer cell, mouse CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002438 NK1.1-positive natural killer cell, mouse CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002438 NK1.1-positive natural killer cell, mouse CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3441,7 +3441,7 @@ CL:0002455 CD8-alpha-negative plasmacytoid dendritic cell CL:4030046 lacks_plasm CL:0002455 CD8-alpha-negative plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002455 CD8-alpha-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002455 CD8-alpha-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002455 CD8-alpha-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002455 CD8-alpha-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002455 CD8-alpha-negative plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000002978 lymphocyte antigen 6G UniProtKB:P35461 CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell RO:0015016 has low plasma membrane amount low False PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) UniProtKB:P20702 UniProtKB:Q9QXH4 IUPHARobj:2454 HGNC:6152 ITGAX CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -3452,7 +3452,7 @@ CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell CL:4030046 lacks_plasm CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive True PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0002456 CD8-alpha-positive plasmacytoid dendritic cell RO:0002104 has plasma membrane part positive False PR:000002978 lymphocyte antigen 6G UniProtKB:P35461 CL:0002457 epidermal Langerhans cell RO:0015015 has high plasma membrane amount high False PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) UniProtKB:P20702 UniProtKB:Q9QXH4 IUPHARobj:2454 HGNC:6152 ITGAX @@ -3463,7 +3463,7 @@ CL:0002457 epidermal Langerhans cell CL:4030046 lacks_plasma_membrane_part negat CL:0002457 epidermal Langerhans cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0002457 epidermal Langerhans cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0002457 epidermal Langerhans cell RO:0002104 has plasma membrane part positive False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0002457 epidermal Langerhans cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002457 epidermal Langerhans cell RO:0002104 has plasma membrane part positive True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002457 epidermal Langerhans cell RO:0002104 has plasma membrane part positive False PR:000001293 C-type lectin domain family 4 member K CD207 (exact) UniProtKB:Q9UJ71 UniProtKB:Q8VBX4 HGNC:17935 CD207 CL:0002458 langerin-positive dermal dendritic cell RO:0015015 has high plasma membrane amount high False PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) UniProtKB:P20702 UniProtKB:Q9QXH4 IUPHARobj:2454 HGNC:6152 ITGAX CL:0002458 langerin-positive dermal dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -3490,7 +3490,7 @@ CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lack CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001003 CD34 molecule CD34 (label) UniProtKB:P28906 UniProtKB:Q64314 PIRSF:PIRSF028749 HGNC:1662 CD34 CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM -CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0002460 CD8-alpha-negative thymic conventional dendritic cell CL:4030046 lacks_plasma_membrane_part negative True PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A @@ -3554,7 +3554,7 @@ CL:0002469 MHC-II-negative classical monocyte RO:0015015 has high plasma membran CL:0002469 MHC-II-negative classical monocyte RO:0015015 has high plasma membrane amount high False PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002469 MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002469 MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002469 MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002469 MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002469 MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002469 MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001206 CX3C chemokine receptor 1 UniProtKB:P49238 UniProtKB:Q9Z0D9 IUPHARobj:74; PIRSF:PIRSF501025 HGNC:2558 CX3CR1 CL:0002469 MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3565,7 +3565,7 @@ CL:0002470 MHC-II-positive classical monocyte RO:0015015 has high plasma membran CL:0002470 MHC-II-positive classical monocyte RO:0015015 has high plasma membrane amount high False PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002470 MHC-II-positive classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002470 MHC-II-positive classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002470 MHC-II-positive classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002470 MHC-II-positive classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002470 MHC-II-positive classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002470 MHC-II-positive classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001206 CX3C chemokine receptor 1 UniProtKB:P49238 UniProtKB:Q9Z0D9 IUPHARobj:74; PIRSF:PIRSF501025 HGNC:2558 CX3CR1 CL:0002470 MHC-II-positive classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3577,7 +3577,7 @@ CL:0002471 MHC-II-negative non-classical monocyte RO:0015016 has low plasma memb CL:0002471 MHC-II-negative non-classical monocyte RO:0015016 has low plasma membrane amount low False PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002471 MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002471 MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002471 MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002471 MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002471 MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002471 MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001199 C-C chemokine receptor type 2 CD192 (exact) UniProtKB:P41597 UniProtKB:P51683 IUPHARobj:59 HGNC:1603 CCR2 CL:0002471 MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3589,7 +3589,7 @@ CL:0002472 MHC-II-low non-classical monocyte RO:0015016 has low plasma membrane CL:0002472 MHC-II-low non-classical monocyte RO:0015016 has low plasma membrane amount low False PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002472 MHC-II-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002472 MHC-II-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002472 MHC-II-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002472 MHC-II-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002472 MHC-II-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002472 MHC-II-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001199 C-C chemokine receptor type 2 CD192 (exact) UniProtKB:P41597 UniProtKB:P51683 IUPHARobj:59 HGNC:1603 CCR2 CL:0002472 MHC-II-low non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3601,7 +3601,7 @@ CL:0002473 MHC-II-high non-classical monocyte RO:0015016 has low plasma membrane CL:0002473 MHC-II-high non-classical monocyte RO:0015016 has low plasma membrane amount low False PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002473 MHC-II-high non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002473 MHC-II-high non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002473 MHC-II-high non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002473 MHC-II-high non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002473 MHC-II-high non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002473 MHC-II-high non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001199 C-C chemokine receptor type 2 CD192 (exact) UniProtKB:P41597 UniProtKB:P51683 IUPHARobj:59 HGNC:1603 CCR2 CL:0002473 MHC-II-high non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3614,7 +3614,7 @@ CL:0002474 lymphoid MHC-II-negative classical monocyte RO:0015015 has high plasm CL:0002474 lymphoid MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002474 lymphoid MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC CL:0002474 lymphoid MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative True PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) UniProtKB:P20702 UniProtKB:Q9QXH4 IUPHARobj:2454 HGNC:6152 ITGAX -CL:0002474 lymphoid MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002474 lymphoid MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002474 lymphoid MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002474 lymphoid MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001206 CX3C chemokine receptor 1 UniProtKB:P49238 UniProtKB:Q9Z0D9 IUPHARobj:74; PIRSF:PIRSF501025 HGNC:2558 CX3CR1 CL:0002474 lymphoid MHC-II-negative classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3627,7 +3627,7 @@ CL:0002475 lymphoid MHC-II-negative non-classical monocyte RO:0015016 has low pl CL:0002475 lymphoid MHC-II-negative non-classical monocyte RO:0015016 has low plasma membrane amount low False PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002475 lymphoid MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0002475 lymphoid MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002475 lymphoid MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002475 lymphoid MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002475 lymphoid MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002475 lymphoid MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001199 C-C chemokine receptor type 2 CD192 (exact) UniProtKB:P41597 UniProtKB:P51683 IUPHARobj:59 HGNC:1603 CCR2 CL:0002475 lymphoid MHC-II-negative non-classical monocyte CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -3636,7 +3636,7 @@ CL:0002475 lymphoid MHC-II-negative non-classical monocyte RO:0002104 has plasma CL:0002475 lymphoid MHC-II-negative non-classical monocyte RO:0002104 has plasma membrane part positive False PR:000001879 leukosialin CD43 (related) UniProtKB:P16150 UniProtKB:P15702 PIRSF:PIRSF001994 HGNC:11249 SPN CL:0002475 lymphoid MHC-II-negative non-classical monocyte RO:0002104 has plasma membrane part positive False PR:000002062 macrophage colony-stimulating factor 1 receptor CD115 (exact) UniProtKB:P07333 UniProtKB:P09581 IUPHARobj:1806; PIRSF:PIRSF500947 HGNC:2433 CSF1R CL:0002476 bone marrow macrophage CL:4030046 lacks_plasma_membrane_part negative False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002476 bone marrow macrophage CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 +CL:0002476 bone marrow macrophage CL:4030046 lacks_plasma_membrane_part negative True PR:000001014 receptor-type tyrosine-protein phosphatase C isoform CD45RABC CD45R (related); CD45RABC (label) UniProtKB:P08575-3 HGNC:9666 PTPRC CL:0002476 bone marrow macrophage CL:4030046 lacks_plasma_membrane_part negative True PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0002476 bone marrow macrophage CL:4030046 lacks_plasma_membrane_part negative True PR:000002980 lymphocyte antigen 6C2 UniProtKB:P0CW03 CL:0002476 bone marrow macrophage RO:0002104 has plasma membrane part positive True PR:000001813 adhesion G protein-coupled receptor E1 UniProtKB:Q14246 UniProtKB:Q61549 IUPHARobj:182; PIRSF:PIRSF038685 HGNC:3336 ADGRE1 @@ -3858,7 +3858,7 @@ CL:0002677 naive regulatory T cell RO:0015016 has low plasma membrane amount low CL:0002677 naive regulatory T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0002677 naive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0002677 naive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001006 receptor-type tyrosine-protein phosphatase C CD45 (related) UniProtKB:P08575 UniProtKB:P06800 IUPHARobj:1852; PIRSF:PIRSF002004 HGNC:9666 PTPRC -CL:0002677 naive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 +CL:0002677 naive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001015 receptor-type tyrosine-protein phosphatase C isoform CD45RA CD45RA (label) UniProtKB:P08575-8 HGNC:9666 PTPRC CL:0002677 naive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001203 C-C chemokine receptor type 7 CD197 (exact); CDw197 (exact) UniProtKB:P32248 UniProtKB:P47774 IUPHARobj:64 HGNC:1608 CCR7 CL:0002677 naive regulatory T cell RO:0002104 has plasma membrane part positive False PR:000001380 interleukin-2 receptor subunit alpha CD25 (exact) UniProtKB:P01589 UniProtKB:P01590 IUPHARobj:1695; PIRSF:PIRSF001954 HGNC:6008 IL2RA CL:0002678 memory regulatory T cell RO:0015016 has low plasma membrane amount low False PR:000001869 interleukin-7 receptor subunit alpha CD127 (exact); CDw127 (exact) UniProtKB:P16871 UniProtKB:P16872 IUPHARobj:1698; PIRSF:PIRSF001960 HGNC:6024 IL7R @@ -3963,8 +3963,8 @@ CL:0017009 Axl+ dendritic cell, human CL:4030046 lacks_plasma_membrane_part nega CL:0017009 Axl+ dendritic cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:0017009 Axl+ dendritic cell, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:0017009 Axl+ dendritic cell, human RO:0002104 has plasma membrane part positive False PR:000002015 MHC class II histocompatibility antigen alpha chain DRA UniProtKB:P01903 HGNC:4947 HLA-DRA -CL:0017009 Axl+ dendritic cell, human RO:0002292 expresses positive True PR:O43699 sialic acid-binding Ig-like lectin 6 (human) CD327 (exact); CD33 (exact); CD33L (related); CD33L1 (related); CDw327 (exact) UniProtKB:O43699-1; UniProtKB:O43699-2; UniProtKB:O43699-3; UniProtKB:O43699-4; UniProtKB:O43699-5; UniProtKB:O43699-6; UniProtKB:O43699 UniProtKB:O43699 -CL:0017009 Axl+ dendritic cell, human RO:0002292 expresses positive True PR:P30530 tyrosine-protein kinase receptor UFO (human) UniProtKB:P30530-1; UniProtKB:P30530-2; UniProtKB:P30530 DTO:03100553; UniProtKB:P30530 +CL:0017009 Axl+ dendritic cell, human RO:0002292 expresses positive True PR:O43699 sialic acid-binding Ig-like lectin 6 (human) CD327 (exact); CD33 (exact); CD33L (related); CD33L1 (related); CDw327 (exact) UniProtKB:O43699-1; UniProtKB:O43699-2; UniProtKB:O43699-3; UniProtKB:O43699-4; UniProtKB:O43699-5; UniProtKB:O43699-6; UniProtKB:O43699 UniProtKB:O43699 HGNC:10875 SIGLEC6 +CL:0017009 Axl+ dendritic cell, human RO:0002292 expresses positive True PR:P30530 tyrosine-protein kinase receptor UFO (human) UniProtKB:P30530-1; UniProtKB:P30530-2; UniProtKB:P30530 DTO:03100553; UniProtKB:P30530 HGNC:905 AXL CL:0019015 lung parenchyma resident eosinophil CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:0019015 lung parenchyma resident eosinophil CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:0019015 lung parenchyma resident eosinophil CL:4030046 lacks_plasma_membrane_part negative False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 @@ -3998,13 +3998,13 @@ CL:0020031 CD8-positive exhausted alpha-beta T cell CL:4030046 lacks_plasma_memb CL:0020031 CD8-positive exhausted alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0020031 CD8-positive exhausted alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001919 programmed cell death protein 1 CD279 (exact) UniProtKB:Q15116 UniProtKB:Q02242 IUPHARobj:2760; PIRSF:PIRSF018380 HGNC:8760 PDCD1 CL:0020031 CD8-positive exhausted alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0020031 CD8-positive exhausted alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0020031 CD8-positive exhausted alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0020033 stem cell memory CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:0020033 stem cell memory CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0020034 stem cell memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:0020034 stem cell memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:0020034 stem cell memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:0020034 stem cell memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:0020034 stem cell memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:0020037 superficial zone articular chondrocyte RO:0002292 expresses positive True PR:000013208 proteoglycan 4 UniProtKB:Q92954 UniProtKB:Q9JM99 HGNC:9364 PRG4 CL:0020039 deep zone articular chondrocyte RO:0002292 expresses positive True PR:000005693 collagen alpha-1(X) chain UniProtKB:Q03692 UniProtKB:Q05306 HGNC:2185 COL10A1 CL:0020040 calcified zone articular chondrocyte RO:0002292 expresses positive True PR:000005693 collagen alpha-1(X) chain UniProtKB:Q03692 UniProtKB:Q05306 HGNC:2185 COL10A1 @@ -4055,7 +4055,7 @@ CL:2000095 cord blood hematopoietic stem cell CL:4030046 lacks_plasma_membrane_p CL:2000095 cord blood hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000002978 lymphocyte antigen 6G UniProtKB:P35461 CL:2000095 cord blood hematopoietic stem cell CL:4030046 lacks_plasma_membrane_part negative False PR:000002981 lymphocyte antigen 76 (mouse) CL:2000096 fibroblast of the reticular layer of dermis RO:0002292 expresses positive False PR:000013031 periostin UniProtKB:Q15063 UniProtKB:Q62009 HGNC:16953 POSTN -CL:2000096 fibroblast of the reticular layer of dermis RO:0002292 expresses positive True PR:Q15063 periostin (human) UniProtKB:Q15063-1; UniProtKB:Q15063-10; UniProtKB:Q15063-2; UniProtKB:Q15063-3; UniProtKB:Q15063-4; UniProtKB:Q15063-5; UniProtKB:Q15063-6; UniProtKB:Q15063-7; UniProtKB:Q15063-8; UniProtKB:Q15063-9; UniProtKB:Q15063 UniProtKB:Q15063 +CL:2000096 fibroblast of the reticular layer of dermis RO:0002292 expresses positive True PR:Q15063 periostin (human) UniProtKB:Q15063-1; UniProtKB:Q15063-10; UniProtKB:Q15063-2; UniProtKB:Q15063-3; UniProtKB:Q15063-4; UniProtKB:Q15063-5; UniProtKB:Q15063-6; UniProtKB:Q15063-7; UniProtKB:Q15063-8; UniProtKB:Q15063-9; UniProtKB:Q15063 UniProtKB:Q15063 HGNC:16953 POSTN CL:4023007 L2/3 bipolar VIP GABAergic interneuron (Mmus) RO:0002292 expresses positive False PR:000017299 VIP peptides UniProtKB:P01282 UniProtKB:P32648 HGNC:12693 VIP CL:4023007 L2/3 bipolar VIP GABAergic interneuron (Mmus) RO:0002292 expresses positive True PR:P32648 VIP peptides (mouse) UniProtKB:P32648-1; UniProtKB:P32648 UniProtKB:P32648 CL:4023010 alpha7 GABAergic cortical interneuron (Mmus) RO:0002292 expresses positive True PR:000005460 neuronal acetylcholine receptor subunit alpha-7 UniProtKB:P36544 UniProtKB:P49582 IUPHARobj:468 @@ -4144,12 +4144,12 @@ CL:4033038 lung resident memory CD4-positive, alpha-beta T cell RO:0002104 has p CL:4033039 lung resident memory CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:4033039 lung resident memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:4033039 lung resident memory CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:4033039 lung resident memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:4033039 lung resident memory CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:4033040 lung resident memory CD8-positive, CD103-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:4033040 lung resident memory CD8-positive, CD103-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive True PR:000001010 integrin alpha-E CD103 (exact) UniProtKB:P38570 UniProtKB:Q60677 IUPHARobj:2450 HGNC:6147 ITGAE CL:4033040 lung resident memory CD8-positive, CD103-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:4033040 lung resident memory CD8-positive, CD103-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:4033040 lung resident memory CD8-positive, CD103-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:4033040 lung resident memory CD8-positive, CD103-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:4033041 CCL3-positive alveolar macrophage RO:0015016 has low plasma membrane amount low False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM CL:4033041 CCL3-positive alveolar macrophage CL:4030046 lacks_plasma_membrane_part negative False PR:000001206 CX3C chemokine receptor 1 UniProtKB:P49238 UniProtKB:Q9Z0D9 IUPHARobj:74; PIRSF:PIRSF501025 HGNC:2558 CX3CR1 CL:4033041 CCL3-positive alveolar macrophage RO:0002104 has plasma membrane part positive False PR:000001013 integrin alpha-X CD11 (exact); CD11C (related); CD11c (exact) UniProtKB:P20702 UniProtKB:Q9QXH4 IUPHARobj:2454 HGNC:6152 ITGAX @@ -4187,7 +4187,7 @@ CL:4033071 cycling natural killer cell CL:4030046 lacks_plasma_membrane_part neg CL:4033074 cycling CD8-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:4033074 cycling CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:4033074 cycling CD8-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:4033074 cycling CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:4033074 cycling CD8-positive, alpha-beta T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:4033075 cycling CD4-positive, alpha-beta T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) CL:4033075 cycling CD4-positive, alpha-beta T cell RO:0002104 has plasma membrane part positive False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:4033077 cycling alveolar macrophage RO:0015016 has low plasma membrane amount low False PR:000001012 integrin alpha-M CD11 (exact); CD11B (related); CD11b (exact) UniProtKB:P11215 UniProtKB:P05555 IUPHARobj:2452 HGNC:6149 ITGAM @@ -4214,7 +4214,7 @@ CL:4033104 superior cervical ganglion TH/NPY neuron RO:0002292 expresses positiv CL:4033104 superior cervical ganglion TH/NPY neuron RO:0002292 expresses positive True PR:000016301 tyrosine 3-monooxygenase UniProtKB:P07101 UniProtKB:P24529 IUPHARobj:1243 HGNC:11782 TH CL:4033105 superior cervical ganglion SST neuron RO:0002292 expresses positive True PR:000015665 somatostatin UniProtKB:P61278 UniProtKB:P60041 HGNC:11329 SST CL:4033106 superior cervical ganglion VIP neuron RO:0002292 expresses positive True PR:000017299 VIP peptides UniProtKB:P01282 UniProtKB:P32648 HGNC:12693 VIP -CL:4033107 superior cervical ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 +CL:4033107 superior cervical ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 HGNC:1437 CALCA CL:4033108 middle cervical ganglion DBH neuron RO:0002292 expresses positive True PR:000006294 dopamine beta-hydroxylase UniProtKB:P09172 UniProtKB:Q64237 IUPHARobj:2486 HGNC:2689 DBH CL:4033109 middle cervical ganglion TH neuron RO:0002292 expresses positive True PR:000016301 tyrosine 3-monooxygenase UniProtKB:P07101 UniProtKB:P24529 IUPHARobj:1243 HGNC:11782 TH CL:4033110 middle cervical ganglion TH/NPY neuron RO:0002292 expresses positive True PR:000011387 neuropeptide Y UniProtKB:P01303 UniProtKB:P57774 HGNC:7955 NPY @@ -4244,7 +4244,7 @@ CL:4033127 lower airway ganglion ChAT/VIP neuron RO:0002292 expresses positive T CL:4033127 lower airway ganglion ChAT/VIP neuron RO:0002292 expresses positive True PR:000017299 VIP peptides UniProtKB:P01282 UniProtKB:P32648 HGNC:12693 VIP CL:4033128 celiac ganglion VIP neuron RO:0002292 expresses positive True PR:000017299 VIP peptides UniProtKB:P01282 UniProtKB:P32648 HGNC:12693 VIP CL:4033129 celiac ganglion PHI neuron RO:0002292 expresses positive True PR:000017299 VIP peptides UniProtKB:P01282 UniProtKB:P32648 HGNC:12693 VIP -CL:4033130 celiac ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 +CL:4033130 celiac ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 HGNC:1437 CALCA CL:4033131 celiac ganglion SP neuron RO:0002292 expresses positive True PR:000016003 protachykinin-1 UniProtKB:P20366 UniProtKB:P41539 HGNC:11517 TAC1 CL:4033132 celiac ganglion SOM neuron RO:0002292 expresses positive True PR:000015665 somatostatin UniProtKB:P61278 UniProtKB:P60041 HGNC:11329 SST CL:4033133 celiac ganglion SOM/CGRP neuron RO:0002292 expresses positive True PR:000004973 calcitonin gene-related peptide type 1 receptor UniProtKB:Q16602 UniProtKB:Q9R1W5 IUPHARobj:47 HGNC:16709 CALCRL @@ -4270,7 +4270,7 @@ CL:4033151 nodose ganglion PVALB neuron RO:0002292 expresses positive True PR:00 CL:4033152 jugular ganglion TRPV1 neuron RO:0002292 expresses positive True PR:000001065 transient receptor potential cation channel TRPV1 UniProtKB:Q8NER1 UniProtKB:Q704Y3 IUPHARobj:507 HGNC:12716 TRPV1 CL:4033153 jugular ganglion TRPV2 neuron RO:0002292 expresses positive True PR:000001064 transient receptor potential cation channel TRPV2 UniProtKB:Q9Y5S1 UniProtKB:Q9WTR1 IUPHARobj:508 HGNC:18082 TRPV2 CL:4033154 jugular ganglion SP neuron RO:0002292 expresses positive True PR:000016003 protachykinin-1 UniProtKB:P20366 UniProtKB:P41539 HGNC:11517 TAC1 -CL:4033155 jugular ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 +CL:4033155 jugular ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 HGNC:1437 CALCA CL:4033156 jugular ganglion SPARCL1 neuron RO:0002292 expresses positive True PR:000015476 SPARC-like protein 1 UniProtKB:Q14515 UniProtKB:P70663 HGNC:11220 SPARCL1 CL:4033157 geniculate ganglion TRPV1 neuron RO:0002292 expresses positive True PR:000001065 transient receptor potential cation channel TRPV1 UniProtKB:Q8NER1 UniProtKB:Q704Y3 IUPHARobj:507 HGNC:12716 TRPV1 CL:4033158 geniculate ganglion SPARCL1 neuron RO:0002292 expresses positive True PR:000015476 SPARC-like protein 1 UniProtKB:Q14515 UniProtKB:P70663 HGNC:11220 SPARCL1 @@ -4301,7 +4301,7 @@ CL:4033173 pelvic ganglion nNOS/VAChT neuron RO:0002292 expresses positive True CL:4033173 pelvic ganglion nNOS/VAChT neuron RO:0002292 expresses positive True PR:000014968 vesicular acetylcholine transporter UniProtKB:Q16572 UniProtKB:O35304 IUPHARobj:1013 HGNC:10936 SLC18A3 CL:4033174 ovarian nerve plexus ganglion TH neuron RO:0002292 expresses positive True PR:000016301 tyrosine 3-monooxygenase UniProtKB:P07101 UniProtKB:P24529 IUPHARobj:1243 HGNC:11782 TH CL:4033175 dorsal root ganglion BRN3A neuron RO:0002292 expresses positive True PR:000013041 POU domain, class 4, transcription factor 1 UniProtKB:Q01851 UniProtKB:P17208 HGNC:9218 POU4F1 -CL:4033176 dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 +CL:4033176 dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 HGNC:1437 CALCA CL:4033177 dorsal root ganglion EDN1 neuron RO:0002292 expresses positive True PR:000006897 endothelin-1 UniProtKB:P05305 UniProtKB:P22387 HGNC:3176 EDN1 CL:4033178 dorsal root ganglion Nav1.7 neuron RO:0002292 expresses positive True PR:000002104 sodium channel protein type 9 subunit alpha UniProtKB:Q15858 UniProtKB:Q62205 IUPHARobj:584 HGNC:10597 SCN9A CL:4033179 dorsal root ganglion Nav1.9 neuron RO:0002292 expresses positive True PR:000002097 sodium channel protein type 11 subunit alpha UniProtKB:Q9UI33 UniProtKB:Q9R053 IUPHARobj:586 HGNC:10583 SCN11A @@ -4363,12 +4363,12 @@ CL:4052020 lung resident granzyme K-associated CD8 T cell RO:0002104 has plasma CL:4052020 lung resident granzyme K-associated CD8 T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:4052020 lung resident granzyme K-associated CD8 T cell RO:0002292 expresses positive False PR:000003472 granzyme K UniProtKB:P49863 UniProtKB:O35205 IUPHARobj:2370 HGNC:4711 GZMK CL:4052020 lung resident granzyme K-associated CD8 T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:4052020 lung resident granzyme K-associated CD8 T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:4052020 lung resident granzyme K-associated CD8 T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:4052021 granzyme K-associated CD8 T cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001004 CD4 molecule CD4 (label) UniProtKB:P01730 UniProtKB:P06332 PIRSF:PIRSF001977 HGNC:1678 CD4 CL:4052021 granzyme K-associated CD8 T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:4052021 granzyme K-associated CD8 T cell RO:0002292 expresses positive True PR:000003472 granzyme K UniProtKB:P49863 UniProtKB:O35205 IUPHARobj:2370 HGNC:4711 GZMK CL:4052021 granzyme K-associated CD8 T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:4052021 granzyme K-associated CD8 T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:4052021 granzyme K-associated CD8 T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:4052028 uterine natural killer cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:4052028 uterine natural killer cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:4052028 uterine natural killer cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 @@ -4377,37 +4377,37 @@ CL:4052032 granzyme H-associated CD8 T cell CL:4030046 lacks_plasma_membrane_par CL:4052032 granzyme H-associated CD8 T cell BFO:0000051 has part positive False PR:000001084 T-cell surface glycoprotein CD8 alpha chain CD8 (label); CD8A (exact); CD8a (exact) UniProtKB:P01732 UniProtKB:P01731 HGNC:1706 CD8A CL:4052032 granzyme H-associated CD8 T cell RO:0002292 expresses positive True PR:000003490 granzyme H UniProtKB:P20718 HGNC:4710 GZMH CL:4052032 granzyme H-associated CD8 T cell RO:0002104 has plasma membrane part positive False PR:000025402 T cell receptor co-receptor CD8 CD8 (label) -CL:4052032 granzyme H-associated CD8 T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 +CL:4052032 granzyme H-associated CD8 T cell BFO:0000051 has part positive False PR:000025403 T-cell surface glycoprotein CD8 alpha chain isoform 1 CD8 (label); CD8A (exact) UniProtKB:P01732-1 HGNC:1706 CD8A CL:4052051 uterine natural killer cell 1, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:4052051 uterine natural killer cell 1, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001010 integrin alpha-E CD103 (exact) UniProtKB:P38570 UniProtKB:Q60677 IUPHARobj:2450 HGNC:6147 ITGAE CL:4052051 uterine natural killer cell 1, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:4052051 uterine natural killer cell 1, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:4052051 uterine natural killer cell 1, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001889 CD14 molecule CD14 (label) UniProtKB:P08571 UniProtKB:P10810 PIRSF:PIRSF002017 HGNC:1628 CD14 -CL:4052051 uterine natural killer cell 1, human CL:4030046 lacks_plasma_membrane_part negative True PR:O95971 CD160 antigen (human) CD160 (label) UniProtKB:O95971-1; UniProtKB:O95971-2; UniProtKB:O95971-3; UniProtKB:O95971-4; UniProtKB:O95971 UniProtKB:O95971 +CL:4052051 uterine natural killer cell 1, human CL:4030046 lacks_plasma_membrane_part negative True PR:O95971 CD160 antigen (human) CD160 (label) UniProtKB:O95971-1; UniProtKB:O95971-2; UniProtKB:O95971-3; UniProtKB:O95971-4; UniProtKB:O95971 UniProtKB:O95971 HGNC:17013 CD160 CL:4052051 uterine natural killer cell 1, human CL:4030046 lacks_plasma_membrane_part negative True PR:P38570 integrin alpha-E (human) CD103 (exact) UniProtKB:P38570 UniProtKB:P38570 HGNC:6147 ITGAE -CL:4052051 uterine natural killer cell 1, human RO:0002104 has plasma membrane part positive True PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) UniProtKB:P49961-1; UniProtKB:P49961-2; UniProtKB:P49961-3; UniProtKB:P49961-4; UniProtKB:P49961-5; UniProtKB:P49961-6; UniProtKB:P49961 UniProtKB:P49961; Reactome:R-HSA-913566 +CL:4052051 uterine natural killer cell 1, human RO:0002104 has plasma membrane part positive True PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) UniProtKB:P49961-1; UniProtKB:P49961-2; UniProtKB:P49961-3; UniProtKB:P49961-4; UniProtKB:P49961-5; UniProtKB:P49961-6; UniProtKB:P49961 UniProtKB:P49961; Reactome:R-HSA-913566 HGNC:3363 ENTPD1 CL:4052051 uterine natural killer cell 1, human RO:0002104 has plasma membrane part positive True PR:P56199 integrin alpha-1 (human) CD49 (exact); CD49a (exact) UniProtKB:P56199 UniProtKB:P56199 HGNC:6134 ITGA1 CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001010 integrin alpha-E CD103 (exact) UniProtKB:P38570 UniProtKB:Q60677 IUPHARobj:2450 HGNC:6147 ITGAE CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001889 CD14 molecule CD14 (label) UniProtKB:P08571 UniProtKB:P10810 PIRSF:PIRSF002017 HGNC:1628 CD14 -CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative True PR:O95971 CD160 antigen (human) CD160 (label) UniProtKB:O95971-1; UniProtKB:O95971-2; UniProtKB:O95971-3; UniProtKB:O95971-4; UniProtKB:O95971 UniProtKB:O95971 +CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative True PR:O95971 CD160 antigen (human) CD160 (label) UniProtKB:O95971-1; UniProtKB:O95971-2; UniProtKB:O95971-3; UniProtKB:O95971-4; UniProtKB:O95971 UniProtKB:O95971 HGNC:17013 CD160 CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative True PR:P38570 integrin alpha-E (human) CD103 (exact) UniProtKB:P38570 UniProtKB:P38570 HGNC:6147 ITGAE -CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative True PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) UniProtKB:P49961-1; UniProtKB:P49961-2; UniProtKB:P49961-3; UniProtKB:P49961-4; UniProtKB:P49961-5; UniProtKB:P49961-6; UniProtKB:P49961 UniProtKB:P49961; Reactome:R-HSA-913566 +CL:4052052 uterine natural killer cell 2, human CL:4030046 lacks_plasma_membrane_part negative True PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) UniProtKB:P49961-1; UniProtKB:P49961-2; UniProtKB:P49961-3; UniProtKB:P49961-4; UniProtKB:P49961-5; UniProtKB:P49961-6; UniProtKB:P49961 UniProtKB:P49961; Reactome:R-HSA-913566 HGNC:3363 ENTPD1 CL:4052052 uterine natural killer cell 2, human RO:0002104 has plasma membrane part positive True PR:P56199 integrin alpha-1 (human) CD49 (exact); CD49a (exact) UniProtKB:P56199 UniProtKB:P56199 HGNC:6134 ITGA1 CL:4052053 uterine natural killer cell 3, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 CL:4052053 uterine natural killer cell 3, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:4052053 uterine natural killer cell 3, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001289 membrane-spanning 4-domains subfamily A member 1 CD20 (exact) UniProtKB:P11836 UniProtKB:P19437 PIRSF:PIRSF001995; IUPHARobj:2628 HGNC:7315 MS4A1 CL:4052053 uterine natural killer cell 3, human CL:4030046 lacks_plasma_membrane_part negative False PR:000001889 CD14 molecule CD14 (label) UniProtKB:P08571 UniProtKB:P10810 PIRSF:PIRSF002017 HGNC:1628 CD14 -CL:4052053 uterine natural killer cell 3, human CL:4030046 lacks_plasma_membrane_part negative True PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) UniProtKB:P49961-1; UniProtKB:P49961-2; UniProtKB:P49961-3; UniProtKB:P49961-4; UniProtKB:P49961-5; UniProtKB:P49961-6; UniProtKB:P49961 UniProtKB:P49961; Reactome:R-HSA-913566 +CL:4052053 uterine natural killer cell 3, human CL:4030046 lacks_plasma_membrane_part negative True PR:P49961 ectonucleoside triphosphate diphosphohydrolase 1 (human) CD39 (related) UniProtKB:P49961-1; UniProtKB:P49961-2; UniProtKB:P49961-3; UniProtKB:P49961-4; UniProtKB:P49961-5; UniProtKB:P49961-6; UniProtKB:P49961 UniProtKB:P49961; Reactome:R-HSA-913566 HGNC:3363 ENTPD1 CL:4052053 uterine natural killer cell 3, human RO:0002104 has plasma membrane part positive False PR:000001010 integrin alpha-E CD103 (exact) UniProtKB:P38570 UniProtKB:Q60677 IUPHARobj:2450 HGNC:6147 ITGAE -CL:4052053 uterine natural killer cell 3, human RO:0002104 has plasma membrane part positive True PR:O95971 CD160 antigen (human) CD160 (label) UniProtKB:O95971-1; UniProtKB:O95971-2; UniProtKB:O95971-3; UniProtKB:O95971-4; UniProtKB:O95971 UniProtKB:O95971 +CL:4052053 uterine natural killer cell 3, human RO:0002104 has plasma membrane part positive True PR:O95971 CD160 antigen (human) CD160 (label) UniProtKB:O95971-1; UniProtKB:O95971-2; UniProtKB:O95971-3; UniProtKB:O95971-4; UniProtKB:O95971 UniProtKB:O95971 HGNC:17013 CD160 CL:4052053 uterine natural killer cell 3, human RO:0002104 has plasma membrane part positive True PR:P38570 integrin alpha-E (human) CD103 (exact) UniProtKB:P38570 UniProtKB:P38570 HGNC:6147 ITGAE CL:4052053 uterine natural killer cell 3, human RO:0002104 has plasma membrane part positive True PR:P56199 integrin alpha-1 (human) CD49 (exact); CD49a (exact) UniProtKB:P56199 UniProtKB:P56199 HGNC:6134 ITGA1 CL:4052055 mature NK T cell, human RO:0002104 has plasma membrane part positive False PR:000001024 neural cell adhesion molecule 1 CD56 (exact) UniProtKB:P13591 UniProtKB:P13595 IUPHARobj:2769 HGNC:7656 NCAM1 CL:4052055 mature NK T cell, human RO:0002104 has plasma membrane part positive False PR:000001874 KLRB1-like protein PIRSF:PIRSF038804 -CL:4052055 mature NK T cell, human RO:0002104 has plasma membrane part positive True PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) UniProtKB:P13591-1; UniProtKB:P13591-2; UniProtKB:P13591-3; UniProtKB:P13591-4; UniProtKB:P13591-5; UniProtKB:P13591-6; UniProtKB:P13591 UniProtKB:P13591 +CL:4052055 mature NK T cell, human RO:0002104 has plasma membrane part positive True PR:P13591 neural cell adhesion molecule 1 (human) CD56 (exact) UniProtKB:P13591-1; UniProtKB:P13591-2; UniProtKB:P13591-3; UniProtKB:P13591-4; UniProtKB:P13591-5; UniProtKB:P13591-6; UniProtKB:P13591 UniProtKB:P13591 HGNC:7656 NCAM1 CL:4052108 IgD-negative class switched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001020 CD3 epsilon CD3 (label); CD3E (exact); CD3e (exact) UniProtKB:P07766 UniProtKB:P22646 IUPHARobj:2742 HGNC:1674 CD3E CL:4052108 IgD-negative class switched memory B cell CL:4030046 lacks_plasma_membrane_part negative False PR:000001935 syndecan-1 CD138 (exact) UniProtKB:P18827 UniProtKB:P18828 PIRSF:PIRSF015854 HGNC:10658 SDC1 CL:4052108 IgD-negative class switched memory B cell RO:0002104 has plasma membrane part positive False PR:000001002 CD19 molecule CD19 (label) UniProtKB:P15391 UniProtKB:P25918 IUPHARobj:2764; PIRSF:PIRSF016630 HGNC:1633 CD19 @@ -4427,7 +4427,7 @@ CL:4072029 pvalb GABAergic interneuron (Homo sapiens) RO:0002292 expresses posit CL:4072031 sst chodl GABAergic interneuron (Homo sapiens) RO:0002292 expresses positive False PR:000005444 chondrolectin UniProtKB:Q9H9P2 UniProtKB:Q9CXM0 HGNC:17807 CHODL CL:4072031 sst chodl GABAergic interneuron (Homo sapiens) RO:0002292 expresses positive False PR:000015665 somatostatin UniProtKB:P61278 UniProtKB:P60041 HGNC:11329 SST CL:4072032 VIP GABAergic interneuron (Homo sapiens) RO:0002292 expresses positive False PR:000017299 VIP peptides UniProtKB:P01282 UniProtKB:P32648 HGNC:12693 VIP -CL:4072032 VIP GABAergic interneuron (Homo sapiens) RO:0002292 expresses positive True PR:P01282 VIP peptides (human) UniProtKB:P01282-1; UniProtKB:P01282-2; UniProtKB:P01282 UniProtKB:P01282 +CL:4072032 VIP GABAergic interneuron (Homo sapiens) RO:0002292 expresses positive True PR:P01282 VIP peptides (human) UniProtKB:P01282-1; UniProtKB:P01282-2; UniProtKB:P01282 UniProtKB:P01282 HGNC:12693 VIP CL:4072034 lamp5 GABAergic interneuron (Homo sapiens) RO:0002292 expresses positive False PR:000032148 lysosome-associated membrane glycoprotein 5 UniProtKB:Q9UJQ1 UniProtKB:Q9D387 HGNC:16097 LAMP5 CL:4072035 sncg GABAergic interneuron (Homo sapiens) RO:0002292 expresses positive False PR:000015325 gamma-synuclein UniProtKB:O76070 UniProtKB:Q9Z0F7 HGNC:11141 SNCG CL:4072035 sncg GABAergic interneuron (Homo sapiens) RO:0002292 expresses positive True PR:O76070 gamma-synuclein (human) UniProtKB:O76070 UniProtKB:O76070 HGNC:11141 SNCG @@ -4437,7 +4437,7 @@ CL:4072046 pvalb chandelier GABAergic interneuron (Homo sapiens) RO:0002292 expr CL:4072104 fibrochondrocyte RO:0002292 expresses positive True PR:000003264 collagen alpha-1(I) chain UniProtKB:P02452 UniProtKB:P11087 HGNC:2197 COL1A1 CL:4072104 fibrochondrocyte RO:0002292 expresses positive True PR:000003328 collagen alpha-1(III) chain UniProtKB:P02461 UniProtKB:P08121 HGNC:2201 COL3A1 CL:4072104 fibrochondrocyte RO:0002292 expresses positive True PR:000003353 collagen alpha-1(VI) chain UniProtKB:P12109 UniProtKB:Q04857 HGNC:2211 COL6A1 -CL:4079000 cervical dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 +CL:4079000 cervical dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 HGNC:1437 CALCA CL:4079001 cervical dorsal root ganglion endothelin-1 neuron RO:0002292 expresses positive True PR:000006897 endothelin-1 UniProtKB:P05305 UniProtKB:P22387 HGNC:3176 EDN1 CL:4079002 cervical dorsal root ganglion Nav1.7 neuron RO:0002292 expresses positive True PR:000002104 sodium channel protein type 9 subunit alpha UniProtKB:Q15858 UniProtKB:Q62205 IUPHARobj:584 HGNC:10597 SCN9A CL:4079003 cervical dorsal root ganglion Nav1.9 neuron RO:0002292 expresses positive True PR:000002097 sodium channel protein type 11 subunit alpha UniProtKB:Q9UI33 UniProtKB:Q9R053 IUPHARobj:586 HGNC:10583 SCN11A @@ -4447,7 +4447,7 @@ CL:4079006 cervical dorsal root ganglion RET neuron RO:0002292 expresses positiv CL:4079007 cervical dorsal root ganglion substance P neuron RO:0002292 expresses positive True PR:000016003 protachykinin-1 UniProtKB:P20366 UniProtKB:P41539 HGNC:11517 TAC1 CL:4079008 cervical dorsal root ganglion TRPV1 neuron RO:0002292 expresses positive True PR:000001065 transient receptor potential cation channel TRPV1 UniProtKB:Q8NER1 UniProtKB:Q704Y3 IUPHARobj:507 HGNC:12716 TRPV1 CL:4079010 intrinsic cardiac ganglion TH neuron RO:0002292 expresses positive True PR:000016301 tyrosine 3-monooxygenase UniProtKB:P07101 UniProtKB:P24529 IUPHARobj:1243 HGNC:11782 TH -CL:4079011 lumbar dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 +CL:4079011 lumbar dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 HGNC:1437 CALCA CL:4079012 lumbar dorsal root ganglion endothelin-1 neuron RO:0002292 expresses positive True PR:000006897 endothelin-1 UniProtKB:P05305 UniProtKB:P22387 HGNC:3176 EDN1 CL:4079013 lumbar dorsal root ganglion Nav1.7 neuron RO:0002292 expresses positive True PR:000002104 sodium channel protein type 9 subunit alpha UniProtKB:Q15858 UniProtKB:Q62205 IUPHARobj:584 HGNC:10597 SCN9A CL:4079014 lumbar dorsal root ganglion Nav1.9 neuron RO:0002292 expresses positive True PR:000002097 sodium channel protein type 11 subunit alpha UniProtKB:Q9UI33 UniProtKB:Q9R053 IUPHARobj:586 HGNC:10583 SCN11A @@ -4456,7 +4456,7 @@ CL:4079016 lumbar dorsal root ganglion Piezo2 neuron RO:0002292 expresses positi CL:4079017 lumbar dorsal root ganglion RET neuron RO:0002292 expresses positive True PR:000013895 proto-oncogene tyrosine-protein kinase receptor Ret UniProtKB:P07949 UniProtKB:P35546 IUPHARobj:2185 HGNC:9967 RET CL:4079018 lumbar dorsal root ganglion substance P neuron RO:0002292 expresses positive True PR:000016003 protachykinin-1 UniProtKB:P20366 UniProtKB:P41539 HGNC:11517 TAC1 CL:4079019 lumbar dorsal root ganglion TRPV1 neuron RO:0002292 expresses positive True PR:000001065 transient receptor potential cation channel TRPV1 UniProtKB:Q8NER1 UniProtKB:Q704Y3 IUPHARobj:507 HGNC:12716 TRPV1 -CL:4079020 sacral dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 +CL:4079020 sacral dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 HGNC:1437 CALCA CL:4079021 sacral dorsal root ganglion endothelin-1 neuron RO:0002292 expresses positive True PR:000006897 endothelin-1 UniProtKB:P05305 UniProtKB:P22387 HGNC:3176 EDN1 CL:4079022 sacral dorsal root ganglion Nav1.7 neuron RO:0002292 expresses positive True PR:000002104 sodium channel protein type 9 subunit alpha UniProtKB:Q15858 UniProtKB:Q62205 IUPHARobj:584 HGNC:10597 SCN9A CL:4079023 sacral dorsal root ganglion Nav1.9 neuron RO:0002292 expresses positive True PR:000002097 sodium channel protein type 11 subunit alpha UniProtKB:Q9UI33 UniProtKB:Q9R053 IUPHARobj:586 HGNC:10583 SCN11A @@ -4465,7 +4465,7 @@ CL:4079025 sacral dorsal root ganglion Piezo2 neuron RO:0002292 expresses positi CL:4079026 sacral dorsal root ganglion RET neuron RO:0002292 expresses positive True PR:000013895 proto-oncogene tyrosine-protein kinase receptor Ret UniProtKB:P07949 UniProtKB:P35546 IUPHARobj:2185 HGNC:9967 RET CL:4079027 sacral dorsal root ganglion substance P neuron RO:0002292 expresses positive True PR:000016003 protachykinin-1 UniProtKB:P20366 UniProtKB:P41539 HGNC:11517 TAC1 CL:4079028 sacral dorsal root ganglion TRPV1 neuron RO:0002292 expresses positive True PR:000001065 transient receptor potential cation channel TRPV1 UniProtKB:Q8NER1 UniProtKB:Q704Y3 IUPHARobj:507 HGNC:12716 TRPV1 -CL:4079029 thoracic dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 +CL:4079029 thoracic dorsal root ganglion CGRP neuron RO:0002292 expresses positive True PR:000027226 calcitonin gene-related peptide 1 UniProtKB:P06881-1 UniProtKB:Q99JA0-1 HGNC:1437 CALCA CL:4079030 thoracic dorsal root ganglion endothelin-1 neuron RO:0002292 expresses positive True PR:000006897 endothelin-1 UniProtKB:P05305 UniProtKB:P22387 HGNC:3176 EDN1 CL:4079031 thoracic dorsal root ganglion Nav1.7 neuron RO:0002292 expresses positive True PR:000002104 sodium channel protein type 9 subunit alpha UniProtKB:Q15858 UniProtKB:Q62205 IUPHARobj:584 HGNC:10597 SCN9A CL:4079032 thoracic dorsal root ganglion Nav1.9 neuron RO:0002292 expresses positive True PR:000002097 sodium channel protein type 11 subunit alpha UniProtKB:Q9UI33 UniProtKB:Q9R053 IUPHARobj:586 HGNC:10583 SCN11A @@ -4515,4 +4515,4 @@ CL:4310137 STRv D1-NUDAP medium spiny neuron (Primate) RO:0002292 expresses posi CL:4310137 STRv D1-NUDAP medium spiny neuron (Primate) RO:0002292 expresses positive False PR:000001177 D(2) dopamine receptor UniProtKB:P14416 UniProtKB:P61168 IUPHARobj:215 HGNC:3023 DRD2 CL:4310137 STRv D1-NUDAP medium spiny neuron (Primate) RO:0002292 expresses positive False PR:000001666 relaxin receptor 1 UniProtKB:Q9HBX9 UniProtKB:Q6R6I7 IUPHARobj:351 HGNC:19718 RXFP1 CL:4310138 STRv D2 medium spiny neuron (Primate) RO:0002292 expresses positive False PR:000001177 D(2) dopamine receptor UniProtKB:P14416 UniProtKB:P61168 IUPHARobj:215 HGNC:3023 DRD2 -CL:7770006 beam B cell, human RO:0002292 expresses positive True PR:Q9UIK5 tomoregulin-2 (human) UniProtKB:Q9UIK5-1; UniProtKB:Q9UIK5-2; UniProtKB:Q9UIK5-3; UniProtKB:Q9UIK5 UniProtKB:Q9UIK5 +CL:7770006 beam B cell, human RO:0002292 expresses positive True PR:Q9UIK5 tomoregulin-2 (human) UniProtKB:Q9UIK5-1; UniProtKB:Q9UIK5-2; UniProtKB:Q9UIK5-3; UniProtKB:Q9UIK5 UniProtKB:Q9UIK5 HGNC:11867 TMEFF2 diff --git a/src/soulcap_cl_mapping/hgnc_map.py b/src/soulcap_cl_mapping/hgnc_map.py index c491d15..54586e9 100644 --- a/src/soulcap_cl_mapping/hgnc_map.py +++ b/src/soulcap_cl_mapping/hgnc_map.py @@ -107,11 +107,36 @@ def extract_hgnc(node: dict[str, Any]) -> tuple[str, str]: return "", "" +def strip_isoform_suffix(curie: str) -> str: + """Strip isoform suffix from a UniProtKB CURIE. + + The Monarch Node Normalizer resolves canonical accessions only; isoform + variants like ``UniProtKB:P16871-1`` must be reduced to ``UniProtKB:P16871`` + before querying. Non-UniProtKB CURIEs are returned unchanged. + + Examples + -------- + >>> strip_isoform_suffix("UniProtKB:P16871-1") + 'UniProtKB:P16871' + >>> strip_isoform_suffix("UniProtKB:P16871") + 'UniProtKB:P16871' + >>> strip_isoform_suffix("PR:000001002") + 'PR:000001002' + """ + if not curie.startswith("UniProtKB:"): + return curie + prefix, accession = curie.split(":", 1) + base = accession.split("-")[0] + return f"{prefix}:{base}" + + def collect_pr_mappings(rows: list[dict[str, str]]) -> dict[str, str]: """Collect unique PR CURIE → first human UniProt CURIE (or "") from the rows. De-duplicates by PR: the first occurrence wins. If ``uniprot_human`` contains several "; "-separated CURIEs, only the first is used for lookup. + Isoform suffixes (e.g. ``-1``, ``-2``) are stripped before returning so + that the Monarch Node Normalizer receives canonical accessions. Returns ------- @@ -125,7 +150,7 @@ def collect_pr_mappings(rows: list[dict[str, str]]) -> dict[str, str]: continue uniprot_human = row.get("uniprot_human", "") first_up = uniprot_human.split(";")[0].strip() if uniprot_human else "" - pr_to_uniprot[pr] = first_up + pr_to_uniprot[pr] = strip_isoform_suffix(first_up) if first_up else "" return pr_to_uniprot diff --git a/tests/test_hgnc_map.py b/tests/test_hgnc_map.py index ee3752c..c3cf1e1 100644 --- a/tests/test_hgnc_map.py +++ b/tests/test_hgnc_map.py @@ -105,6 +105,31 @@ def test_extract_hgnc_missing_label() -> None: assert symbol == "" +# --------------------------------------------------------------------------- # +# strip_isoform_suffix (pure) +# --------------------------------------------------------------------------- # + + +def test_strip_isoform_suffix_removes_suffix() -> None: + assert hgnc_map.strip_isoform_suffix("UniProtKB:P16871-1") == "UniProtKB:P16871" + + +def test_strip_isoform_suffix_no_suffix() -> None: + assert hgnc_map.strip_isoform_suffix("UniProtKB:P16871") == "UniProtKB:P16871" + + +def test_strip_isoform_suffix_multi_digit() -> None: + assert hgnc_map.strip_isoform_suffix("UniProtKB:P08575-10") == "UniProtKB:P08575" + + +def test_strip_isoform_suffix_non_uniprot_unchanged() -> None: + assert hgnc_map.strip_isoform_suffix("PR:000001002") == "PR:000001002" + + +def test_strip_isoform_suffix_empty_string() -> None: + assert hgnc_map.strip_isoform_suffix("") == "" + + # --------------------------------------------------------------------------- # # collect_pr_mappings (pure) # --------------------------------------------------------------------------- # @@ -141,6 +166,13 @@ def test_collect_pr_mappings_multi_uniprot_takes_first() -> None: assert result == {"PR:000001002": "UniProtKB:P15391"} +def test_collect_pr_mappings_strips_isoform_suffix() -> None: + """Isoform suffix is stripped so Monarch receives the canonical accession.""" + rows = [{"pr": "PR:000001015", "uniprot_human": "UniProtKB:P08575-8"}] + result = hgnc_map.collect_pr_mappings(rows) + assert result == {"PR:000001015": "UniProtKB:P08575"} + + def test_collect_pr_mappings_no_uniprot() -> None: rows = [{"pr": "PR:000002981", "uniprot_human": ""}] result = hgnc_map.collect_pr_mappings(rows)