From f5d994ffe199afe39a2c73c031c78829b8e3a5ee Mon Sep 17 00:00:00 2001 From: swalpe <61828940+swalpe@users.noreply.github.com> Date: Mon, 24 Aug 2026 17:35:54 +0200 Subject: [PATCH 1/5] Update CellNames_scseqCMs6_sigs.gmt Updated ionocyte signature after review --- besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt b/besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt index d553a3b2..04aafe55 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt +++ b/besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt @@ -103,7 +103,7 @@ Pneumocyte Genes used for automatic annotation of scRNA-seq derived clusters of Club Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. SCGB1A1 BPIFB1 TMEM45A SCGB3A2 CiliatedEpithelial Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. RSPH1 CCDC17 CAPS ODF3B ODF3B FAM183A FOXJ1 CCDC78 Basal Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. KRT5 TP63 -Ionocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. CHGA CALCA ASCL1 +Ionocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. Updated Aug 26 ASCL3 BSND FOXI1 CLCNKB STAP1 ProlifMonocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. MKI67 PCNA STMN1 HMGB2 ILC2 Genes used for automatic annotation of scRNA-seq derived clusters of Intestine (v8 May20) derived by Schwalie P. GATA3 RORA IL2RA IL1RL1 IL7R FAM102A ProlifMyeloid Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. MKI67 PCNA STMN1 HMGB2 From cce00c0f685523630d7c9ca8f4904fe6fd3496be Mon Sep 17 00:00:00 2001 From: swalpe <61828940+swalpe@users.noreply.github.com> Date: Mon, 24 Aug 2026 17:38:52 +0200 Subject: [PATCH 2/5] Update CellNames_scseqCMs6_sigs.mouse.gmt Also updated mouse sig to match updated human sig --- besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt b/besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt index 46be2303..0157cdd8 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt +++ b/besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt @@ -103,7 +103,7 @@ Pneumocyte Genes used for automatic annotation of scRNA-seq derived clusters of Club Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Scgb1a1 Bpifb1 Tmem45a Scgb3a2 CiliatedEpithelial Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Rsph1 Ccdc17 Odf3b Odf3b Fam183b Foxj1 Ccdc78 Basal Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Krt5 Trp63 -Ionocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Chga Calca Ascl1 +Ionocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS. Updated Aug26 Ascl3 Bsnd Foxi1 Clcnkb Stap1 ProlifMonocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Mki67 Pcna Stmn1 Hmgb2 ILC2 Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Gata3 Rora Il2ra Il1rl1 Il7r Fam102a ProlifMyeloid Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Mki67 Pcna Stmn1 Hmgb2 From 9d25dc4f46d7301d3ed13033396d6b40deab49e3 Mon Sep 17 00:00:00 2001 From: swalpe <61828940+swalpe@users.noreply.github.com> Date: Tue, 25 Aug 2026 12:44:05 +0200 Subject: [PATCH 3/5] Update CellNames_scseqCMs6_Extrasigs.gmt Added neuroendocrine at extrasig gmt --- besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt | 1 + 1 file changed, 1 insertion(+) diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt b/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt index 0f5f3bdb..8416485f 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt +++ b/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt @@ -34,3 +34,4 @@ MAIT Additional genes (less specific or lower expressed) whose expression can al HEVEndothelial Additional genes (less specific or lower expressed) whose expression can also be inspected; Endothelial-specific genes curated based on literature and scRNA-seq expression; derived by Schwalie P. and Bianchi R. FUT7 RAB3C CLEC7A ADGR6 CDKN3 CCL23 CCL14 MelMelanoma Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. MIA TYR SLC45A2 CDH19 PMEL SLC24A5 MAGEA6 GJB1 PLP1 PRAME CAPN3 ERBB3 GPM6B S100B PAX3 S100A1 MLANA ColorectalCancer Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. S100P CEACAM6 DPEP1 MAL2 REG4 +Neuroendocrine Genes cross-checked with Onecellatlas and schub (Aug26) derived by Schwalie P. ASCL1 CALCA CHGA CHGB GRP UCHL1 NRXN1 From d1c3cb4060f29fb20cb3ac13c6ce875cf33eb7b3 Mon Sep 17 00:00:00 2001 From: swalpe <61828940+swalpe@users.noreply.github.com> Date: Tue, 25 Aug 2026 12:45:19 +0200 Subject: [PATCH 4/5] Update CellNames_scseqCMs6_Extrasigs.gmt Fixed signature naming to correspond to extrasig convention --- .../genesets/CellNames_scseqCMs6_Extrasigs.gmt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt b/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt index 8416485f..5b022a80 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt +++ b/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt @@ -30,8 +30,8 @@ Fibroblast_scv Additional genes (less specific) used for automatic annotation of InflamFibroblast_scv Additional genes (less specific) used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS MMP2 RARRES2 NNMT CXCL6 Macrophage_CXCL9_scv Additional genes (less specific) used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS FCGR3A SLAMF8 CALHM6 FCGR1A LILRB1 Platelet_scv Additional genes (less specific) used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS ITGA2B GP1BA CTTN LCN2 F13A1 CLU -MAIT Additional genes (less specific or lower expressed) whose expression can also be inspected. Derived by LAS IL7R IL18R1 CCR5 DPP4 -HEVEndothelial Additional genes (less specific or lower expressed) whose expression can also be inspected; Endothelial-specific genes curated based on literature and scRNA-seq expression; derived by Schwalie P. and Bianchi R. FUT7 RAB3C CLEC7A ADGR6 CDKN3 CCL23 CCL14 -MelMelanoma Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. MIA TYR SLC45A2 CDH19 PMEL SLC24A5 MAGEA6 GJB1 PLP1 PRAME CAPN3 ERBB3 GPM6B S100B PAX3 S100A1 MLANA -ColorectalCancer Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. S100P CEACAM6 DPEP1 MAL2 REG4 -Neuroendocrine Genes cross-checked with Onecellatlas and schub (Aug26) derived by Schwalie P. ASCL1 CALCA CHGA CHGB GRP UCHL1 NRXN1 +MAIT_scv Additional genes (less specific or lower expressed) whose expression can also be inspected. Derived by LAS IL7R IL18R1 CCR5 DPP4 +HEVEndothelial_scv Additional genes (less specific or lower expressed) whose expression can also be inspected; Endothelial-specific genes curated based on literature and scRNA-seq expression; derived by Schwalie P. and Bianchi R. FUT7 RAB3C CLEC7A ADGR6 CDKN3 CCL23 CCL14 +MelMelanoma_scv Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. MIA TYR SLC45A2 CDH19 PMEL SLC24A5 MAGEA6 GJB1 PLP1 PRAME CAPN3 ERBB3 GPM6B S100B PAX3 S100A1 MLANA +ColorectalCancer_scv Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. S100P CEACAM6 DPEP1 MAL2 REG4 +Neuroendocrine_scv Genes cross-checked with Onecellatlas and schub (Aug26) derived by Schwalie P. ASCL1 CALCA CHGA CHGB GRP UCHL1 NRXN1 From 372f4128e03947ab5dc8ae26d0486e2b4ee4a1a6 Mon Sep 17 00:00:00 2001 From: swalpe <61828940+swalpe@users.noreply.github.com> Date: Tue, 25 Aug 2026 12:52:12 +0200 Subject: [PATCH 5/5] Update CellNames_scseqCMs6_Extrasigs.mouse.gmt Update mouse neuroendocrine sig as well --- .../genesets/CellNames_scseqCMs6_Extrasigs.mouse.gmt | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.mouse.gmt b/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.mouse.gmt index e37ff707..ffcade8b 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.mouse.gmt +++ b/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.mouse.gmt @@ -24,6 +24,7 @@ Macrophage_RETNLA_scv Additional genes (less specific) used for automatic annota MonocyteDC_scv Additional genes (less specific) used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS C5ar1 Clec4e Il1rn Lst1 Macrophage_MSR1_scv Additional genes (less specific) used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Msr1 Cbr2 Gpr84 Mertk Ccl7 Igf1 Arg1 C3ar1 C1qc C1qa ResourceCD8Tcell_scv Additional genes (less specific) used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Rasgrp2 Gm26740 Klrg1 Klf3 Klf2 Gm2682 Gm45552 -MAIT Additional genes (less specific or lower expressed) whose expression can also be inspected. Derived by LAS Il7r Il18r1 Ccr5 Dpp4 -MelMelanoma Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Gm21983 Tyr Slc45a2 Cdh19 Pmel Slc24a5 Gjb1 Plp1 Capn3 Erbb3 Gpm6b S100b Pax3 S100a1 Mlana -ColorectalCancer Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Ceacam2 Dpep1 Mal2 Reg4 Gm40318 +MAIT_scv Additional genes (less specific or lower expressed) whose expression can also be inspected. Derived by LAS Il7r Il18r1 Ccr5 Dpp4 +MelMelanoma_scv Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Gm21983 Tyr Slc45a2 Cdh19 Pmel Slc24a5 Gjb1 Plp1 Capn3 Erbb3 Gpm6b S100b Pax3 S100a1 Mlana +ColorectalCancer_scv Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Ceacam2 Dpep1 Mal2 Reg4 Gm40318 +Neuroendocrine_scv Genes checked in OneCellatlas and scHub (Aug26) for human by PCS Ascl1 Calca Chga Chgb Grp Uchl1 Nrxn1