Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/research/ilc_dc/SHA256SUMS

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+3929775c224d6c57e05726a2c2e09905ae1d9067b285295916f20f818e047a0c  REPORT.md
+8e79b301a67baca19ff7a442d8282e4d7e2d7f622bcc737af692073d9ef1fffc  SEARCH_LOG.md
+043714c740224317d869068752633881a3ecba751abacf71a209e551d76bc520  build_evidence.py
+3ba6ea33508cd94a0688c8551bea4ee4b4d4ccffc3976cd3ffbb4eb3018e7737  core_panels.csv
+4069ab07b995115741cc7649c36ba7e7366e9ab715f1bf5c3b49191cce7b8c61  evidence.csv
+76f7b9db90b6ec0319b0f68dc3e380dd852bb2dc2776b936b9149859453ed296  protected_sentinels.csv
+dfd15507a57237785fee64c224ca51f2b29acf63991778dd8994d5abf5abf5bb  references.json
+95600c5b7cfa2e3ff7a81d70d67ac1a0af3bd60b891e0e7c96680d4bc46b3cbf  source_manifest.json
+e6fc335e9de6cbfbd33cca0ac31331f2a0f7a74764324cc0f0f8a77a240f3c8f  sources/Bourdely_TableS1.xlsx
+1bbe9fd529fb4a03676c776d712709b44e5d47ed2a63a632b0bd596cabbc0e4f  sources/Bourdely_supp_europe.zip
+dd632be07ed5c0921236d11432b69933ca28445e480bc8273d5202770655fb02  sources/Dutertre2019_mmc2.xlsx
+b302e0fe93b5ed493dfae0e47e313dab9121524e1ec743d5df1d804f953f81d2  sources/Lim2017_author.pdf
+a019e4991bbabf25106e5668491fd08beff144ce6c7793769792b87ddc9e6013  sources/Lim2017_author.txt
+2a976730e9a7ec23d7db3795e2e4ee41e145e7dfda55ffd0f05dd7fb627dbe9d  sources/Lim2017_mmc2.xlsx
+a1a73194958f6cc97d6701a50cdc429bba1d6960e8142f3fb703c81b342b8323  sources/Lim2017_mmc3.xlsx
+a905db7b157bb16eb7b19793db2cec22ec961e281adb7fc1e9207a19d6bb9f89  sources/Lim2017_mmc4.xlsx
+59f58a7d461026b9b1fba1eb0c31454ef8d52fa32afa26d145e93dceee23b633  sources/Lim2017_mmc5.xlsx
+0695c2b24b8b9cb68ca9d0eea158ea1a26f239108beb3c6c0ce18111a28d648e  sources/Maier.html
+620c14adb9b543f264bf24fb406d7ca69f55a6a1dbca676e689400631b699f90  sources/Maier.txt
+e28cc4a7e2c3b3d4beebac8a58cd9f768c6f1723c73d2b1104d03f56d55a1d36  sources/Maier_TableS1.xlsx
+743241bda0ef010a3889da236c14163269de44ec323df29e7e38ad95d4b84d5f  sources/Maier_TableS2.xlsx
+cdfd8bef5d8dbf0124cfea331d33ee23d8362552f257faf18ef9e2ed345f839d  sources/Maier_nature.html
+e7d66bdd082a7924c36ef755a873c1d3588efb587b4c22de873d80512fb2a43e  sources/Mazzurana_DataS1_alt.xlsx
+ac95b150350c8ba6d6d9acb42c8e6ba6490249b2db63e111729dcfa44456c386  sources/Mazzurana_DataS2_alt.xlsx
+ece312d6fdfa47ca882f5f521ed0a63cc1d7986d101e1516b60e4af7550b3ca6  sources/Mazzurana_supp.zip
+edd45a2293a986d2a653391ffe2d5160b7c4106e373f2834e2b03a57e7344364  sources/PMC7445430.txt
+6582dba5cc969832abaa06546c623c2d50134cd4a93832db054fadf6271c7e7b  sources/PMC7445430.xml
+7e043d6b8ee3f3fa3d3134a1588061026d20d148643aeb1fe11f724e27f3eaa8  sources/PMC8089104.txt
+089739be5b392477e9179f09d1092924d51b42dbccd7f92ca96dd9dff0a4cc01  sources/PMC8089104.xml
+d44d83330d874cae9273e62771f60ce6de5c7eb4a278e4fe8d4a269909741d7c  sources/Transitional2023.html
+c09de996f4265e53d40100c6246f04fb3be41d6af3d534411fb3886e864b6c54  sources/Transitional2023.txt
+13573a08e1feb7b543188fbf41c08b835d8350435299e08b4e8f3c8bb6d825b7  sources/Villani.html
+5e08eebdedb9824a6ce2160135bbd6cb00340ec7f486414b2133fb5d283f83b3  sources/Villani.txt
+805c085cf30bec86eab87e0b050cc0ee165d06fc1d65d850c0637581477dedad  sources/Villani_Tables1-16.xlsx
+51416c41b91de53c8252625a78c8539081a716c8e1823e295772ce228ecdbbcd  sources/Villani_supp_europe.zip
+5c90bbea5ebe9ec5e7687528ffe3965550fd8b9ab98646f0161e1e184aad7ea2  summary.json
+e67075e045d5c16919dec55df8c3f1db741c6d98ec8107dbc68337b9d1782184  verification.json

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/research/ilc_dc/build_evidence.py

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+"""Extract source-verified human ILC/DC candidate programs (CPU-only)."""
+from pathlib import Path
+import csv
+import json
+import zipfile
+from lxml import etree
+from collections import defaultdict
+import openpyxl
+
+ROOT = Path(__file__).resolve().parent
+SRC = ROOT / "sources"
+FIELDS = "gene_symbol population role priority source_url primary_source_url doi source_locator evidence_note context tissue tissue_scope verification_status source_id program assay direction source_gene_symbol source_statistic evidence_level evaluation_role endpoint_informed".split()
+ROWS = []
+REFS = {
+    "Mazzurana2021": {"doi": "10.1038/s41422-020-00445-x", "url": "https://www.nature.com/articles/s41422-020-00445-x", "title": "Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing"},
+    "Bourdely2020": {"doi": "10.1016/j.immuni.2020.06.002", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/", "title": "Transcriptional and Functional Analysis of CD1c+ Human Dendritic Cells Identifies a CD163+ Subset Priming CD8+CD103+ T Cells"},
+    "Villani2017": {"doi": "10.1126/science.aah4573", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/", "title": "Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes and progenitors"},
+    "Maier2020": {"doi": "10.1038/s41586-020-2134-y", "url": "https://www.nature.com/articles/s41586-020-2134-y", "title": "A conserved dendritic-cell regulatory program limits antitumour immunity"},
+    "Lim2017": {"doi": "10.1016/j.cell.2017.02.021", "url": "https://www.sciencedirect.com/science/article/pii/S009286741730199X", "title": "Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation"},
+    "Dutertre2019": {"doi": "10.1016/j.immuni.2019.08.008", "url": "https://www.sciencedirect.com/science/article/pii/S1074761319303346", "title": "Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells"},
+    "Sulczewski2023": {"doi": "10.1038/s41590-023-01545-7", "url": "https://www.nature.com/articles/s41590-023-01545-7", "title": "Transitional dendritic cells are distinct from conventional DC2 precursors and mediate proinflammatory antiviral responses"},
+    "Bernink2013": {"doi": "10.1038/ni.2534", "url": "https://www.nature.com/articles/ni.2534", "title": "Human type 1 innate lymphoid cells accumulate in inflamed mucosal tissues"},
+    "Konya2018": {"doi": "10.1016/j.jaci.2017.01.045", "url": "https://pubmed.ncbi.nlm.nih.gov/28433688/", "title": "Vitamin D downregulates the IL-23 receptor pathway in human mucosal group 3 innate lymphoid cells"},
+}
+
+def add(genes, population, role, priority, source_id, locator, note, tissue="blood", program="", assay="RNA", direction="positive", status="verified_article", stats="", level="primary_article", context="human primary cells"):
+    if isinstance(genes, str):
+        genes = genes.split()
+    ref = REFS[source_id]
+    for gene in genes:
+        if not isinstance(gene, str) or not gene.strip():
+            continue
+        ROWS.append(dict(zip(FIELDS, [gene, population, role, priority, ref["url"], ref["url"], ref["doi"], locator, note, context, tissue, tissue, status, source_id, program or population, assay, direction, gene, stats, level, "available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity", "not_known; flag if this source also defines benchmark endpoint"])))
+
+add("GATA3 MAF HPGD HPGDS MBOAT2 IL9R", "ILC2", "identity", "core", "Mazzurana2021", "Fig.4b; Results: Gene modules reveal subset- and tissue-specific profiles of ILC2", "Author-described ILC2 core transcriptome across blood/tonsil/lung. None is an individually sufficient classifier.", "blood;tonsil;lung", "ILC2_core")
+add("PTGDR2 S1PR2 CCR2 TNFSF10 TNFRSF19 CD200R1", "ILC2", "identity", "core", "Mazzurana2021", "Fig.4b", "Blood or blood/tonsil enriched ILC2 receptors and regulatory transcripts; PTGDR2 encodes CRTH2 and may decrease after alarmin activation.", "blood;tonsil", "blood_ILC2")
+add("IL10RA KLRG1 PTGER2 ANXA1 LGALS1", "ILC2", "state", "supporting", "Mazzurana2021", "Fig.4b; module17", "Less ILC2-restricted module of potential negative regulation; shared genes are not specific identity evidence.", "blood;tonsil;lung", "ILC2_regulation")
+add("IL13 IL1RL1 IL17RB SLAMF1 TNFRSF9 FFAR3 PPARG", "ILC2_activated", "state", "optional_tissue", "Mazzurana2021", "Fig.4b module65; Fig.5", "Lung ILC2 program; alarmin-treated blood ILC2 acquire IL1RL1/IL17RB protein and reduce CRTH2. Not universal resting blood requirements.", "lung;in-vitro-alarmin-treated-blood", "alarmin_ILC2")
+add("RORC AHR KIT IL1R1 ICOS CCR6 TNFSF11 TNFSF4 CD96 CD81 PTPN22 LIF", "ILC3", "identity", "optional_tissue", "Mazzurana2021", "Fig.3b; module3", "Author-described ILC3-enriched transcripts, especially colon; blood KIT+ cells may be nILC/ILCP rather than mature ILC3.", "colon;lung;tonsil", "ILC3_lineage")
+add("NCR2 IL23R NRP1 IKZF2 TNFSF13B CCL20 JAML PECAM1 TOX RBPJ CD300LF IL4I1", "ILC3", "identity", "optional_tissue", "Mazzurana2021", "Fig.3b", "Colon/tonsil ILC3 transcript program; tissue-specific support, not constitutive blood ILC3 panel.", "colon;tonsil", "ILC3_tissue")
+add("IL22 CSF2 CXCL8 VEGFA BHLHE40 BCL2A1 LTA4H LTB4R", "ILC3_activated", "state", "optional_tissue", "Mazzurana2021", "Fig.3b,e-h", "ILC3 effector/metabolic/tissue programs; cytokine absence in unstimulated sparse RNA does not exclude ILC3.", "colon;lung", "ILC3_effector")
+add("AREG", "tissue_ILC_activation", "state", "optional_tissue", "Mazzurana2021", "Fig.2d module7; Results Migration- and tissue-resident transcriptional profiles", "RNA tissue-residency/activation module includes AREG. Shared repair/activation signal, not ILC2-specific and not required in resting blood.", "colon;lung;tonsil", "ILC_tissue_repair")
+add("IL17F", "ILC3_activated", "state", "optional_tissue", "Konya2018", "Primary abstract Results; article ELISA and multiplex immunoassay methods", "Human tonsil/gut ILC3 functional IL-17F production after IL-23 plus IL-1beta, reduced with1,25D. Protein-level functional sentinel; no claim that resting PBMC ILC must express detectable IL17F RNA.", "tonsil;gut;in-vitro-cytokine-stimulation", "ILC3_IL17F_function", assay="protein_ELISA", status="verified_primary_abstract_and_methods")
+add("TCF7", "ILCP_naive_ILC", "identity", "core", "Mazzurana2021", "Results ILC3 section; Supplementary DataS1", "Blood nILC TF; shared with T cells, so use joint ILC and T-lineage evidence.", "blood", "ILCP_naive_ILC")
+add("CD3D CD3E CD3G CD4 CD5 CD6 CD27 LEF1 CD8A EOMES", "ILC1_T_NK_boundary", "disambiguation", "core", "Mazzurana2021", "Figs.6-7", "Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.", "blood;tonsil", "T_ILC_boundary", direction="alternative_lineage_evidence")
+add("SELL S1PR1 LDHB ICAM3 S100A4 S100A6 S100A11 ITGB2 ITGAL ITGAM", "circulating_ILC", "state", "supporting", "Mazzurana2021", "Fig.2d modules11,23,41", "Blood/tonsil migratory program shared by nILC and mature ILC, not ILC-specific.", "blood;tonsil", "ILC_circulation")
+add("CLEC10A FCER1A CD74 HLA-DRA", "DC3_cDC2", "identity", "core", "Bourdely2020", "Fig.1D-E; Results DC3 identification", "RNA DC program shared by cDC2 and DC3; use with monocyte contrast.", "blood", "DC3_shared_DC")
+add("CD14 S100A8 S100A9 S100A12 VCAN", "DC3_monocyte_boundary", "disambiguation", "core", "Bourdely2020", "Fig.1D-F", "DC3 shares these with monocytes; CD14/S100A8/S100A9 alone cannot label DC3.", "blood", "DC3_monocyte_shared")
+add("C5AR1 SOD2 RBP7", "monocyte_vs_DC3", "disambiguation", "core", "Bourdely2020", "Fig.1D-E", "RNA enriched/restricted to monocyte cluster C in this experiment; CD88 protein=C5AR1. Low RNA alone is not proof of protein negativity.", "blood", "monocyte_exclusion_from_DC3", direction="monocyte_positive_DC3_low")
+add("CD163 BTLA CD5 CD1C", "DC3_cDC2", "disambiguation", "core", "Bourdely2020", "Fig.1G-H; paragraph on scRNA detection", "CD88-CD1c+BTLA-CD163+ DC3 vs BTLA+CD163- cDC2; CD163/BTLA/CD5 protein informative despite not detected in their scRNA analysis. Do not require RNA detection in every cell.", "blood", "DC3_protein_boundary", assay="protein;bulkRNA_supported_for_CD163", direction="contrast_dependent")
+add("ID2 GATA3 TOX TCF7 ETS1 RORA ZBTB16 NOTCH1 IKZF1 CD2 CD7 IL7R", "ILCP_naive_ILC", "identity", "core", "Lim2017", "Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs", "Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.", "blood", "ILCP_commitment", assay="bulkRNA;H3K4me2_for_subset")
+add("KIT IL7R CD7 IL1R1", "ILCP_naive_ILC", "identity", "core", "Lim2017", "Fig.1A-C and S1", "Lin-CD7+CD127+CD117+ blood population with IL-1R1 surface expression; KIT alone does not make a mature ILC3.", "blood", "ILCP_surface_phenotype", assay="protein")
+add("PTGDR2 CD34 NCR2 NCAM1 CD69", "ILCP_naive_ILC", "disambiguation", "supporting", "Lim2017", "Fig.1 and S1", "Blood ILCP sorting/phenotype is CRTH2-CD34-CD56-, unlike activated tissue ILCs; protein-negative gates cannot be translated to RNA hard zeros.", "blood", "ILCP_surface_exclusions", assay="protein", direction="negative_in_source_phenotype")
+add("RAG1 RAG2 EBF1 CD3E BCL11A LMO2", "ILCP_T_B_progenitor_boundary", "disambiguation", "supporting", "Lim2017", "Fig.S2B; main text p1090", "Authors did not detect these T/B developmental transcripts in CD117+ ILCP versus HSC context. Absence in sparse scRNA is not lineage proof; adult-versus-fetal distinction matters.", "blood", "ILCP_T_B_exclusion", direction="not_detected_in_bulk_source")
+add("EOMES TBX21 RORC CCR6 IL1RL1 IL23R IFNG IL13 IL5 IL22 IL17A", "ILCP_vs_mature_ILC", "disambiguation", "supporting", "Lim2017", "Fig.2F and S2; main text p1090", "Mature-lineage TF/receptor/cytokine transcripts lacked notable expression in blood ILCP despite poised chromatin. Do not require mature cytokines to recognize ILCP.", "blood", "ILCP_maturation_boundary", direction="low_in_ILCP_mature_program")
+add("CLEC9A CADM1 XCR1", "cDC1", "identity", "core", "Villani2017", "Fig.1; TableS2; Results six DC subsets", "CLEC9A discriminates source DC1; THBD/CD141 alone shared with pDC and ASDC. CADM1/XCR1 support multi-gene classification.", "blood", "cDC1_identity")
+add("AXL SIGLEC6 SIGLEC1 CD22 PPP1R14A DAB2 S100A10 FAM105A MED12L ALDH2 LTK", "ASDC_AXL_SIGLEC6", "identity", "core", "Villani2017", "Fig.4A,D and TableS2; Fig.4D top-ten purity genes", "Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.", "blood", "ASDC_identity")
+add("TCF4 IRF7 TLR7 SLC15A4 PACSIN1 DERL3 LAMP5 SCAMP5 SLA2 PTCRA PTPRCAP", "pDC", "identity", "core", "Villani2017", "Fig.5A and S6A", "Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).", "blood", "pDC_identity")
+add("IL3RA CLEC4C NRP1 MZB1 ITGAX IFI30 LY86 GLIPR2 FGR LYZ ENTPD1 CD2 CX3CR1 CD33 CD5", "pDC_ASDC_cDC_boundary", "disambiguation", "core", "Villani2017", "Figs.4D-E and 5A", "IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.", "blood", "pDC_ASDC_boundary", direction="contrast_dependent")
+add("C5AR1 FCAR FCER1A CD5 CD163 CD14", "DC3_cDC2_monocyte_boundary", "disambiguation", "core", "Dutertre2019", "Abstract and Figs.1,6", "CD88=C5AR1 and CD89=FCAR distinguish monocytes; Fc-epsilon-RI-alpha=FCER1A and HLA-DQ support cDC2 compartment; CD5/CD163/CD14 resolve its subsets. Original study integrates protein/RNA, but these boundary rules are primarily protein phenotypes.", "blood;tissues", "blood_DC_monocyte_boundary", assay="protein;integratedRNA", direction="contrast_dependent", status="verified_primary_article_text")
+add("AXL SIGLEC6 IL3RA CD5 CD1C CD33 SIRPA CLEC9A CD14 CD163", "ASDC_tDC_cDC2_transition", "disambiguation", "supporting", "Sulczewski2023", "Fig.4i-k; human sorting methods", "Human blood AXL+SIGLEC6+ tDC after2d culture gain CD33/CD172a(SIRPA)/CD1c/CD5 without CLEC9A/CD14/CD163 upregulation. tDC/ASDC should not be automatically collapsed into all pre-cDC; culture evidence does not prove a blood snapshot trajectory.", "blood;in-vitro-culture", "ASDC_tDC_ontology", assay="protein_CyTOF", direction="contrast_and_transition_dependent")
+add("IL1B", "ASDC_tDC_activated", "state", "optional_state", "Sulczewski2023", "Fig.8l-n; human experiments", "Human tDC produce IL-1beta after CpG/influenza/CMV stimuli; functional protein evidence, not a constitutive resting tDC RNA marker.", "blood_in-vitro-viral-stimulation", "tDC_viral_state", assay="protein")
+add("TBX21 IFNG", "ILC1_tissue", "identity", "optional_tissue", "Bernink2013", "Abstract; main Figs.2,5", "Human tonsil/inflamed gut ILC1 expresses T-bet and responds to IL-12 with IFN-gamma. Shared with NK/T; does not establish pure circulating ILC1.", "tonsil;inflamed-intestine", "ILC1_type1", assay="RNA;protein", status="verified_primary_abstract_and_figure_description")
+add("PRF1 GZMB NCAM1 FCGR3A KLRD1", "ILC1_NK_boundary", "disambiguation", "optional_tissue", "Bernink2013", "Abstract", "This tissue ILC1 population lacked perforin/granzymeB/CD56/CD16/CD94 relative to NK. Protein-based source contrast; do not use as universal exclusion of every ILC1-like or activated population.", "tonsil;inflamed-intestine", "ILC1_vs_NK_source_specific", assay="protein", direction="negative_in_source_ILC1", status="verified_primary_abstract")
+
+w = openpyxl.load_workbook(SRC / "Mazzurana_DataS1_alt.xlsx", read_only=True, data_only=True)
+modules = defaultdict(list)
+for g, m in list(w["DE_modules"].values)[1:]:
+    if g:
+        modules[int(m)].append(g)
+module_specs = {
+    50: ("ILC2", "identity", "supporting", "blood;tonsil;lung", "ILC2_module50"),
+    17: ("ILC2_regulation", "state", "supporting", "blood;tonsil;lung", "ILC2_module17"),
+    28: ("NK_ILC1_boundary", "disambiguation", "supporting", "blood;tonsil;lung;colon", "cytotoxic_NK_module28"),
+    32: ("ILC1_T_boundary", "disambiguation", "supporting", "blood;tonsil", "T_like_module32"),
+    3: ("ILC3", "identity", "optional_tissue", "colon;lung;tonsil", "ILC3_module3"),
+    13: ("ILC3", "identity", "optional_tissue", "colon;tonsil", "ILC3_module13"),
+    65: ("ILC2_activated", "state", "optional_tissue", "lung", "alarmin_ILC2_module65"),
+}
+for m, (pop, role, pri, tissue, program) in module_specs.items():
+    add(modules[m], pop, role, pri, "Mazzurana2021", f"Supplementary DataS1 sheet DE_modules module {m}; Figs.3-6", "Exact author WGCNA module members. Modules were built from permissive DE input (absolute log2FC>0.1, nominal p<0.1 per sheet header), not all members individually specific or FDR-significant. Coexpression program candidate, not universal hard gate.", tissue, program, status="verified_downloaded_table", level="primary_supplement_program")
+
+for sheet in ["SelectedTranscriptBlood_fc>0.5", "SelectedTranscriptnILC_fc>0.5"]:
+    for i, r in enumerate(list(w[sheet].values)[1:], start=2):
+        if len(r)<8 or not r[7] or r[6] not in ["B_ILC2", "B_nILC"]:
+            continue
+        pop = "ILC2" if r[6] == "B_ILC2" else "ILCP_naive_ILC"
+        stats = json.dumps(dict(zip(["p_val","avg_logFC","pct.1","pct.2","p_val_adj"],r[1:6])), separators=(",",":"))
+        add([r[7]], pop, "identity", "supporting", "Mazzurana2021", f"Supplementary DataS1 sheet {sheet} Excel row {i}; cluster {r[6]}", "Exact published selected-transcript row; gene taken from named gene column, not suffixed row names. Candidate expression program; not automatically core or specific. Recorded source statistics are not an independent validation.", "blood", f"{r[6]}_published_selected_transcripts", status="verified_downloaded_table", stats=stats, level="primary_supplement_ranked")
+
+# Lim RNA/ChIP overlap is an exact published 398-member list. It is broad ILC
+# commitment versus HSC, not a 398-gene discriminator against mature T/NK.
+lim = openpyxl.load_workbook(SRC/"Lim2017_mmc3.xlsx", read_only=True, data_only=True)
+lim_genes = [r[0] for r in list(lim.active.values)[1:] if r[0]]
+assert len(lim_genes) == 398
+add(lim_genes, "ILCP_naive_ILC", "identity", "supporting", "Lim2017", "Supplement mmc3.xlsx Sheet1 rows2-399; header 398 common elements in RNA-Seq and ChIP-Seq; Fig.2E/TableS3 cited in article", "Exact RNA-high/chromatin overlap program (398 genes). Comparison with CD34+ HSCs supports ILC commitment but does not establish specificity against mature T/NK. No de novo FDR filter applied.", "blood", "ILCP_RNA_chromatin_398", assay="bulkRNA;H3K4me2", status="verified_downloaded_table", level="primary_supplement_program")
+
+villani = openpyxl.load_workbook(SRC/"Villani_Tables1-16.xlsx", read_only=True, data_only=True)
+dc_labels = {"DC1":"cDC1","DC2":"cDC2","DC3":"DC3_CD1C_B","DC4":"DC4_monocyte_boundary","DC5":"ASDC_AXL_SIGLEC6","DC6":"pDC"}
+for i,r in enumerate(list(villani["TableS2.Allmarkers"].values),1):
+    if len(r)<10 or r[8] not in dc_labels or not isinstance(r[1],str): continue
+    cluster = r[8]
+    stats=json.dumps(dict(zip(["rank","AUC","avg_diff","power","pct1","pct2","p_value"],[r[0],*r[2:8]])),separators=(",",":"))
+    role="disambiguation" if cluster in ["DC3","DC4","DC5"] else "identity"
+    add([r[1]], dc_labels[cluster], role, "supporting", "Villani2017", f"TableS2.Allmarkers Excel row {i}; original cluster {cluster}", "Exact published ranked blood DC discriminator. Whole table retained, not every row meets paper's highlighted AUC>=0.85 set. Original symbols and statistics preserved; validate modern aliases and lineage specificity. DC3/4 labels are study-specific and require current ontology mapping.", "blood", f"Villani_{cluster}_ranked", status="verified_downloaded_table", stats=stats, level="primary_supplement_ranked")
+for sheet,pop in [("TableS3.CD1C subsets","cDC2_DC3_boundary"),("TableS6.DC3.vsMono1","DC3_monocyte_boundary")]:
+    for i,r in enumerate(list(villani[sheet].values),1):
+        if len(r)<8 or not isinstance(r[7],str) or not r[7].startswith("Higher"): continue
+        stats=json.dumps(dict(zip(["AUC","avg_diff","power","pct1","pct2","p_value"],r[1:7])),separators=(",",":"))
+        add([r[0]],pop,"disambiguation","supporting","Villani2017",f"{sheet} Excel row {i}",r[7]+". Published contrast, not universal exclusion. Original symbol preserved for integrator alias validation.","blood",sheet,status="verified_downloaded_table",stats=stats,direction=r[7],level="primary_supplement_ranked")
+
+# Bourdely supplement uses Strict OOXML, unsupported by this openpyxl version.
+# Read cells from original ZIP XML without modifying the publisher file.
+def strict_sheets(path):
+    with zipfile.ZipFile(path) as z:
+        strings=["".join(x.itertext()) for x in etree.fromstring(z.read("xl/sharedStrings.xml"))]
+        rels={x.get("Id"):x.get("Target") for x in etree.fromstring(z.read("xl/_rels/workbook.xml.rels"))}
+        wb=etree.fromstring(z.read("xl/workbook.xml"))
+        for s in wb.xpath('//*[local-name()="sheet"]'):
+            rid=next(v for k,v in s.attrib.items() if k.endswith("}id"))
+            root=etree.fromstring(z.read("xl/"+rels[rid]));rows=[]
+            for row in root.xpath('//*[local-name()="sheetData"]/*'):
+                values={}
+                for c in row:
+                    v=c.find("{*}v")
+                    if v is None:continue
+                    t=v.text
+                    if c.get("t")=="s":t=strings[int(t)]
+                    values[''.join(x for x in c.get('r') if x.isalpha())]=t
+                rows.append((int(row.get("r")),values))
+            yield s.get("name"),rows
+
+for sheet,rs in strict_sheets(SRC/"Bourdely_TableS1.xlsx"):
+    if sheet not in ["DC3 vs cDC2 CD5neg_Blood","DC3 vs cDC2 CD5pos_Blood","DC3 vs Mono_Blood","cDC2+TLR vs DC3+TLR_Blood","DC3+TLR vs Mono+TLR_Blood"]:continue
+    state="TLR" in sheet
+    for i,r in rs:
+        if i<4 or not r.get('A') or not r.get('D','').startswith('higher'):continue
+        comment=r['D'];gene=r['A']
+        stats=json.dumps({"log2FC":r.get('B'),"padj":r.get('C')},separators=(",",":"))
+        pop="DC3" if "DC3" in comment else ("monocyte" if "Monocyte" in comment else "cDC2")
+        add([gene],pop+("_TLR_activated" if state else ""),"state" if state else "disambiguation","optional_state" if state else "supporting","Bourdely2020",f"TableS1 sheet {sheet} Excel row {i}",comment+". Exact author-supplied significant DE row; contrast and direction retained. Shared inflammatory or antibody genes are not automatically lineage-specific; do not turn all DEGs into hard gates.","blood_in-vitro-TLR" if state else "blood",sheet,assay="bulkRNA",direction=comment,status="verified_downloaded_table",stats=stats,level="primary_supplement_ranked")
+
+maier=openpyxl.load_workbook(SRC/"Maier_TableS2.xlsx",read_only=True,data_only=True)
+for i,r in enumerate(maier.active.values,1):
+    if len(r)<4 or r[2]!="human":continue
+    pop={"human DC1 genes":"cDC1","human DC2 genes":"cDC2","human mregDC genes":"mregDC_state"}[r[0]]
+    add([g.strip() for g in r[3].split(',')],pop,"state" if "mreg" in pop else "identity","optional_tissue","Maier2020",f"TableS2 Sheet1 Excel row {i}; {r[0]}; Fig.4d", "Exact author HUMAN scoring list; mouse rows excluded. Lung/tumor context, heterogeneous broad program including shared/proliferation genes. mregDC is a maturation/regulatory state accessible from multiple cDC lineages, not blood DC3.","lung;NSCLC",r[0].replace(' ','_'),status="verified_downloaded_table",level="primary_supplement_program")
+
+def write():
+    seen=set(); unique=[]
+    for r in ROWS:
+        key=(r['gene_symbol'],r['population'],r['source_id'],r['source_locator'])
+        if key not in seen: unique.append(r);seen.add(key)
+    with (ROOT/"evidence.csv").open("w",newline="") as f:
+        out=csv.DictWriter(f,fieldnames=FIELDS);out.writeheader();out.writerows(unique)
+    (ROOT/"references.json").write_text(json.dumps(REFS,indent=2)+"\n")
+    print(json.dumps({"rows":len(unique),"unique_genes":len({r['gene_symbol'] for r in unique}),"sources":len({r['source_id'] for r in unique})}))
+
+if __name__ == "__main__":
+    write()

paper-releases/pbisc-diffusion/updates/20261015T141849Z-rare-cell-7k-8k-panels/diffusion/dataset/server_1/model8/plans/rare_gene_context_expansion_20261015/research/ilc_dc/core_panels.csv

@@ -0,0 +1,102 @@
+gene_symbol,population,role,priority,source_url,primary_source_url,doi,source_locator,evidence_note,context,tissue,tissue_scope,verification_status,source_id,program,assay,direction,source_gene_symbol,source_statistic,evidence_level,evaluation_role,endpoint_informed
+GATA3,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b; Results: Gene modules reveal subset- and tissue-specific profiles of ILC2,Author-described ILC2 core transcriptome across blood/tonsil/lung. None is an individually sufficient classifier.,human primary cells,blood;tonsil;lung,blood;tonsil;lung,verified_article,Mazzurana2021,ILC2_core,RNA,positive,GATA3,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+MAF,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b; Results: Gene modules reveal subset- and tissue-specific profiles of ILC2,Author-described ILC2 core transcriptome across blood/tonsil/lung. None is an individually sufficient classifier.,human primary cells,blood;tonsil;lung,blood;tonsil;lung,verified_article,Mazzurana2021,ILC2_core,RNA,positive,MAF,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+HPGD,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b; Results: Gene modules reveal subset- and tissue-specific profiles of ILC2,Author-described ILC2 core transcriptome across blood/tonsil/lung. None is an individually sufficient classifier.,human primary cells,blood;tonsil;lung,blood;tonsil;lung,verified_article,Mazzurana2021,ILC2_core,RNA,positive,HPGD,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+HPGDS,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b; Results: Gene modules reveal subset- and tissue-specific profiles of ILC2,Author-described ILC2 core transcriptome across blood/tonsil/lung. None is an individually sufficient classifier.,human primary cells,blood;tonsil;lung,blood;tonsil;lung,verified_article,Mazzurana2021,ILC2_core,RNA,positive,HPGDS,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+MBOAT2,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b; Results: Gene modules reveal subset- and tissue-specific profiles of ILC2,Author-described ILC2 core transcriptome across blood/tonsil/lung. None is an individually sufficient classifier.,human primary cells,blood;tonsil;lung,blood;tonsil;lung,verified_article,Mazzurana2021,ILC2_core,RNA,positive,MBOAT2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+IL9R,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b; Results: Gene modules reveal subset- and tissue-specific profiles of ILC2,Author-described ILC2 core transcriptome across blood/tonsil/lung. None is an individually sufficient classifier.,human primary cells,blood;tonsil;lung,blood;tonsil;lung,verified_article,Mazzurana2021,ILC2_core,RNA,positive,IL9R,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+PTGDR2,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b,Blood or blood/tonsil enriched ILC2 receptors and regulatory transcripts; PTGDR2 encodes CRTH2 and may decrease after alarmin activation.,human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,blood_ILC2,RNA,positive,PTGDR2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+S1PR2,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b,Blood or blood/tonsil enriched ILC2 receptors and regulatory transcripts; PTGDR2 encodes CRTH2 and may decrease after alarmin activation.,human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,blood_ILC2,RNA,positive,S1PR2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CCR2,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b,Blood or blood/tonsil enriched ILC2 receptors and regulatory transcripts; PTGDR2 encodes CRTH2 and may decrease after alarmin activation.,human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,blood_ILC2,RNA,positive,CCR2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+TNFSF10,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b,Blood or blood/tonsil enriched ILC2 receptors and regulatory transcripts; PTGDR2 encodes CRTH2 and may decrease after alarmin activation.,human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,blood_ILC2,RNA,positive,TNFSF10,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+TNFRSF19,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b,Blood or blood/tonsil enriched ILC2 receptors and regulatory transcripts; PTGDR2 encodes CRTH2 and may decrease after alarmin activation.,human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,blood_ILC2,RNA,positive,TNFRSF19,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD200R1,ILC2,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Fig.4b,Blood or blood/tonsil enriched ILC2 receptors and regulatory transcripts; PTGDR2 encodes CRTH2 and may decrease after alarmin activation.,human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,blood_ILC2,RNA,positive,CD200R1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+TCF7,ILCP_naive_ILC,identity,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Results ILC3 section; Supplementary DataS1,"Blood nILC TF; shared with T cells, so use joint ILC and T-lineage evidence.",human primary cells,blood,blood,verified_article,Mazzurana2021,ILCP_naive_ILC,RNA,positive,TCF7,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD3D,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,CD3D,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD3E,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,CD3E,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD3G,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,CD3G,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD4,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,CD4,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD5,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,CD5,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD6,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,CD6,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD27,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,CD27,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+LEF1,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,LEF1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD8A,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,CD8A,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+EOMES,ILC1_T_NK_boundary,disambiguation,core,https://www.nature.com/articles/s41422-020-00445-x,https://www.nature.com/articles/s41422-020-00445-x,10.1038/s41422-020-00445-x,Figs.6-7,"Putative blood/tonsil ILC1 and EOMES+ILC1 carry T-cell-like programs; many have rearranged TCR. Retain genes to resolve ambiguous identity, not as positive proof of pure ILC1.",human primary cells,blood;tonsil,blood;tonsil,verified_article,Mazzurana2021,T_ILC_boundary,RNA,alternative_lineage_evidence,EOMES,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CLEC10A,DC3_cDC2,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-E; Results DC3 identification,RNA DC program shared by cDC2 and DC3; use with monocyte contrast.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_shared_DC,RNA,positive,CLEC10A,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+FCER1A,DC3_cDC2,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-E; Results DC3 identification,RNA DC program shared by cDC2 and DC3; use with monocyte contrast.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_shared_DC,RNA,positive,FCER1A,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD74,DC3_cDC2,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-E; Results DC3 identification,RNA DC program shared by cDC2 and DC3; use with monocyte contrast.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_shared_DC,RNA,positive,CD74,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+HLA-DRA,DC3_cDC2,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-E; Results DC3 identification,RNA DC program shared by cDC2 and DC3; use with monocyte contrast.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_shared_DC,RNA,positive,HLA-DRA,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD14,DC3_monocyte_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-F,DC3 shares these with monocytes; CD14/S100A8/S100A9 alone cannot label DC3.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_monocyte_shared,RNA,positive,CD14,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+S100A8,DC3_monocyte_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-F,DC3 shares these with monocytes; CD14/S100A8/S100A9 alone cannot label DC3.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_monocyte_shared,RNA,positive,S100A8,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+S100A9,DC3_monocyte_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-F,DC3 shares these with monocytes; CD14/S100A8/S100A9 alone cannot label DC3.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_monocyte_shared,RNA,positive,S100A9,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+S100A12,DC3_monocyte_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-F,DC3 shares these with monocytes; CD14/S100A8/S100A9 alone cannot label DC3.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_monocyte_shared,RNA,positive,S100A12,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+VCAN,DC3_monocyte_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-F,DC3 shares these with monocytes; CD14/S100A8/S100A9 alone cannot label DC3.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_monocyte_shared,RNA,positive,VCAN,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+C5AR1,monocyte_vs_DC3,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-E,RNA enriched/restricted to monocyte cluster C in this experiment; CD88 protein=C5AR1. Low RNA alone is not proof of protein negativity.,human primary cells,blood,blood,verified_article,Bourdely2020,monocyte_exclusion_from_DC3,RNA,monocyte_positive_DC3_low,C5AR1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+SOD2,monocyte_vs_DC3,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-E,RNA enriched/restricted to monocyte cluster C in this experiment; CD88 protein=C5AR1. Low RNA alone is not proof of protein negativity.,human primary cells,blood,blood,verified_article,Bourdely2020,monocyte_exclusion_from_DC3,RNA,monocyte_positive_DC3_low,SOD2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+RBP7,monocyte_vs_DC3,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1D-E,RNA enriched/restricted to monocyte cluster C in this experiment; CD88 protein=C5AR1. Low RNA alone is not proof of protein negativity.,human primary cells,blood,blood,verified_article,Bourdely2020,monocyte_exclusion_from_DC3,RNA,monocyte_positive_DC3_low,RBP7,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD163,DC3_cDC2,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1G-H; paragraph on scRNA detection,CD88-CD1c+BTLA-CD163+ DC3 vs BTLA+CD163- cDC2; CD163/BTLA/CD5 protein informative despite not detected in their scRNA analysis. Do not require RNA detection in every cell.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_protein_boundary,protein;bulkRNA_supported_for_CD163,contrast_dependent,CD163,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+BTLA,DC3_cDC2,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1G-H; paragraph on scRNA detection,CD88-CD1c+BTLA-CD163+ DC3 vs BTLA+CD163- cDC2; CD163/BTLA/CD5 protein informative despite not detected in their scRNA analysis. Do not require RNA detection in every cell.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_protein_boundary,protein;bulkRNA_supported_for_CD163,contrast_dependent,BTLA,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD5,DC3_cDC2,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1G-H; paragraph on scRNA detection,CD88-CD1c+BTLA-CD163+ DC3 vs BTLA+CD163- cDC2; CD163/BTLA/CD5 protein informative despite not detected in their scRNA analysis. Do not require RNA detection in every cell.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_protein_boundary,protein;bulkRNA_supported_for_CD163,contrast_dependent,CD5,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD1C,DC3_cDC2,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,https://pmc.ncbi.nlm.nih.gov/articles/PMC7445430/,10.1016/j.immuni.2020.06.002,Fig.1G-H; paragraph on scRNA detection,CD88-CD1c+BTLA-CD163+ DC3 vs BTLA+CD163- cDC2; CD163/BTLA/CD5 protein informative despite not detected in their scRNA analysis. Do not require RNA detection in every cell.,human primary cells,blood,blood,verified_article,Bourdely2020,DC3_protein_boundary,protein;bulkRNA_supported_for_CD163,contrast_dependent,CD1C,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+ID2,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,ID2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+GATA3,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,GATA3,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+TOX,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,TOX,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+TCF7,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,TCF7,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+ETS1,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,ETS1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+RORA,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,RORA,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+ZBTB16,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,ZBTB16,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+NOTCH1,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,NOTCH1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+IKZF1,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,IKZF1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD2,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,CD2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD7,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,CD7,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+IL7R,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.2D-E and S2A-B; Results Transcription and Chromatin Landscapes of CD117+ ILCs,"Adult circulating CD117+ ILCP RNA and/or RNA-ChIP concordance relative to CD34+ HSCs. Shared lymphoid genes require T/NK exclusions. This supports lineage commitment, not mature ILC subtype sufficiency.",human primary cells,blood,blood,verified_article,Lim2017,ILCP_commitment,bulkRNA;H3K4me2_for_subset,positive,IL7R,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+KIT,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.1A-C and S1,Lin-CD7+CD127+CD117+ blood population with IL-1R1 surface expression; KIT alone does not make a mature ILC3.,human primary cells,blood,blood,verified_article,Lim2017,ILCP_surface_phenotype,protein,positive,KIT,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+IL7R,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.1A-C and S1,Lin-CD7+CD127+CD117+ blood population with IL-1R1 surface expression; KIT alone does not make a mature ILC3.,human primary cells,blood,blood,verified_article,Lim2017,ILCP_surface_phenotype,protein,positive,IL7R,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD7,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.1A-C and S1,Lin-CD7+CD127+CD117+ blood population with IL-1R1 surface expression; KIT alone does not make a mature ILC3.,human primary cells,blood,blood,verified_article,Lim2017,ILCP_surface_phenotype,protein,positive,CD7,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+IL1R1,ILCP_naive_ILC,identity,core,https://www.sciencedirect.com/science/article/pii/S009286741730199X,https://www.sciencedirect.com/science/article/pii/S009286741730199X,10.1016/j.cell.2017.02.021,Fig.1A-C and S1,Lin-CD7+CD127+CD117+ blood population with IL-1R1 surface expression; KIT alone does not make a mature ILC3.,human primary cells,blood,blood,verified_article,Lim2017,ILCP_surface_phenotype,protein,positive,IL1R1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CLEC9A,cDC1,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.1; TableS2; Results six DC subsets,CLEC9A discriminates source DC1; THBD/CD141 alone shared with pDC and ASDC. CADM1/XCR1 support multi-gene classification.,human primary cells,blood,blood,verified_article,Villani2017,cDC1_identity,RNA,positive,CLEC9A,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CADM1,cDC1,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.1; TableS2; Results six DC subsets,CLEC9A discriminates source DC1; THBD/CD141 alone shared with pDC and ASDC. CADM1/XCR1 support multi-gene classification.,human primary cells,blood,blood,verified_article,Villani2017,cDC1_identity,RNA,positive,CADM1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+XCR1,cDC1,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.1; TableS2; Results six DC subsets,CLEC9A discriminates source DC1; THBD/CD141 alone shared with pDC and ASDC. CADM1/XCR1 support multi-gene classification.,human primary cells,blood,blood,verified_article,Villani2017,cDC1_identity,RNA,positive,XCR1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+AXL,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,AXL,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+SIGLEC6,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,SIGLEC6,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+SIGLEC1,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,SIGLEC1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD22,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,CD22,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+PPP1R14A,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,PPP1R14A,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+DAB2,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,DAB2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+S100A10,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,S100A10,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+FAM105A,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,FAM105A,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+MED12L,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,MED12L,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+ALDH2,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,ALDH2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+LTK,ASDC_AXL_SIGLEC6,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,"Fig.4A,D and TableS2; Fig.4D top-ten purity genes",Exact article AS-DC signature; ASDC=DC5 in this paper. These span pDC-like to cDC-like states; AXL alone also marks other DC states.,human primary cells,blood,blood,verified_article,Villani2017,ASDC_identity,RNA,positive,LTK,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+TCF4,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,TCF4,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+IRF7,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,IRF7,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+TLR7,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,TLR7,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+SLC15A4,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,SLC15A4,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+PACSIN1,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,PACSIN1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+DERL3,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,DERL3,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+LAMP5,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,LAMP5,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+SCAMP5,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,SCAMP5,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+SLA2,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,SLA2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+PTCRA,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,PTCRA,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+PTPRCAP,pDC,identity,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Fig.5A and S6A,"Author-described pDC program separating pDC from ASDC: sensing/IFN, secretion and TCF4 targets. TCF4 here is E2-2 (not TCF7L2).",human primary cells,blood,blood,verified_article,Villani2017,pDC_identity,RNA,positive,PTPRCAP,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+IL3RA,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,IL3RA,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CLEC4C,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,CLEC4C,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+NRP1,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,NRP1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+MZB1,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,MZB1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+ITGAX,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,ITGAX,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+IFI30,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,IFI30,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+LY86,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,LY86,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+GLIPR2,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,GLIPR2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+FGR,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,FGR,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+LYZ,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,LYZ,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+ENTPD1,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,ENTPD1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD2,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,CD2,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CX3CR1,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,CX3CR1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD33,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,CD33,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD5,pDC_ASDC_cDC_boundary,disambiguation,core,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,https://pmc.ncbi.nlm.nih.gov/articles/PMC5775029/,10.1126/science.aah4573,Figs.4D-E and 5A,"IL3RA/CLEC4C shared between pDC and pDC-like ASDC; cDC-like and pDC-like ASDC continuum. Evaluate paired positive/alternative programs, not one shared receptor.",human primary cells,blood,blood,verified_article,Villani2017,pDC_ASDC_boundary,RNA,contrast_dependent,CD5,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+C5AR1,DC3_cDC2_monocyte_boundary,disambiguation,core,https://www.sciencedirect.com/science/article/pii/S1074761319303346,https://www.sciencedirect.com/science/article/pii/S1074761319303346,10.1016/j.immuni.2019.08.008,"Abstract and Figs.1,6","CD88=C5AR1 and CD89=FCAR distinguish monocytes; Fc-epsilon-RI-alpha=FCER1A and HLA-DQ support cDC2 compartment; CD5/CD163/CD14 resolve its subsets. Original study integrates protein/RNA, but these boundary rules are primarily protein phenotypes.",human primary cells,blood;tissues,blood;tissues,verified_primary_article_text,Dutertre2019,blood_DC_monocyte_boundary,protein;integratedRNA,contrast_dependent,C5AR1,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+FCAR,DC3_cDC2_monocyte_boundary,disambiguation,core,https://www.sciencedirect.com/science/article/pii/S1074761319303346,https://www.sciencedirect.com/science/article/pii/S1074761319303346,10.1016/j.immuni.2019.08.008,"Abstract and Figs.1,6","CD88=C5AR1 and CD89=FCAR distinguish monocytes; Fc-epsilon-RI-alpha=FCER1A and HLA-DQ support cDC2 compartment; CD5/CD163/CD14 resolve its subsets. Original study integrates protein/RNA, but these boundary rules are primarily protein phenotypes.",human primary cells,blood;tissues,blood;tissues,verified_primary_article_text,Dutertre2019,blood_DC_monocyte_boundary,protein;integratedRNA,contrast_dependent,FCAR,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+FCER1A,DC3_cDC2_monocyte_boundary,disambiguation,core,https://www.sciencedirect.com/science/article/pii/S1074761319303346,https://www.sciencedirect.com/science/article/pii/S1074761319303346,10.1016/j.immuni.2019.08.008,"Abstract and Figs.1,6","CD88=C5AR1 and CD89=FCAR distinguish monocytes; Fc-epsilon-RI-alpha=FCER1A and HLA-DQ support cDC2 compartment; CD5/CD163/CD14 resolve its subsets. Original study integrates protein/RNA, but these boundary rules are primarily protein phenotypes.",human primary cells,blood;tissues,blood;tissues,verified_primary_article_text,Dutertre2019,blood_DC_monocyte_boundary,protein;integratedRNA,contrast_dependent,FCER1A,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD5,DC3_cDC2_monocyte_boundary,disambiguation,core,https://www.sciencedirect.com/science/article/pii/S1074761319303346,https://www.sciencedirect.com/science/article/pii/S1074761319303346,10.1016/j.immuni.2019.08.008,"Abstract and Figs.1,6","CD88=C5AR1 and CD89=FCAR distinguish monocytes; Fc-epsilon-RI-alpha=FCER1A and HLA-DQ support cDC2 compartment; CD5/CD163/CD14 resolve its subsets. Original study integrates protein/RNA, but these boundary rules are primarily protein phenotypes.",human primary cells,blood;tissues,blood;tissues,verified_primary_article_text,Dutertre2019,blood_DC_monocyte_boundary,protein;integratedRNA,contrast_dependent,CD5,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD163,DC3_cDC2_monocyte_boundary,disambiguation,core,https://www.sciencedirect.com/science/article/pii/S1074761319303346,https://www.sciencedirect.com/science/article/pii/S1074761319303346,10.1016/j.immuni.2019.08.008,"Abstract and Figs.1,6","CD88=C5AR1 and CD89=FCAR distinguish monocytes; Fc-epsilon-RI-alpha=FCER1A and HLA-DQ support cDC2 compartment; CD5/CD163/CD14 resolve its subsets. Original study integrates protein/RNA, but these boundary rules are primarily protein phenotypes.",human primary cells,blood;tissues,blood;tissues,verified_primary_article_text,Dutertre2019,blood_DC_monocyte_boundary,protein;integratedRNA,contrast_dependent,CD163,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint
+CD14,DC3_cDC2_monocyte_boundary,disambiguation,core,https://www.sciencedirect.com/science/article/pii/S1074761319303346,https://www.sciencedirect.com/science/article/pii/S1074761319303346,10.1016/j.immuni.2019.08.008,"Abstract and Figs.1,6","CD88=C5AR1 and CD89=FCAR distinguish monocytes; Fc-epsilon-RI-alpha=FCER1A and HLA-DQ support cDC2 compartment; CD5/CD163/CD14 resolve its subsets. Original study integrates protein/RNA, but these boundary rules are primarily protein phenotypes.",human primary cells,blood;tissues,blood;tissues,verified_primary_article_text,Dutertre2019,blood_DC_monocyte_boundary,protein;integratedRNA,contrast_dependent,CD14,,primary_article,available_for_model_and_validation; predeclare independent held-out validation sets to avoid circularity,not_known; flag if this source also defines benchmark endpoint