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Move malignant signatures from main sigs to Extrasigs #391

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Merged
hatjek merged 1 commit into from
Jun 29, 2026
Merged

Move malignant signatures from main sigs to Extrasigs #391

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3 changes: 2 additions & 1 deletion besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt
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Expand Up @@ -32,4 +32,5 @@ Macrophage_CXCL9_scv Additional genes (less specific) used for automatic annotat
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
2 changes: 2 additions & 0 deletions besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.mouse.gmt
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Expand Up @@ -25,3 +25,5 @@ MonocyteDC_scv Additional genes (less specific) used for automatic annotation of
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
1 change: 0 additions & 1 deletion besca/datasets/genesets/CellNames_scseqCMs6_config.mouse.tsv
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Expand Up @@ -4,7 +4,6 @@ Fibroblast None 2.75 2
Endothelial None 2.5 3
Epithelial None 2.5 4
Granulocyte Myeloid 0.1 21
Malignant None 2.5 60
MemBcell Bcell 1.5 8
Myeloid Hematopoietic 0.5 12.5
NKcell Hematopoietic 1.5 10.2
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1 change: 0 additions & 1 deletion besca/datasets/genesets/CellNames_scseqCMs6_config.tsv
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Expand Up @@ -4,7 +4,6 @@ Fibroblast None 3 2
Endothelial None 2 3
Epithelial None 1.75 4
Granulocyte Myeloid 0.05 21
Malignant None 2 60
MemBcell Bcell 1.5 8
Myeloid Hematopoietic 0.5 12.5
NKcell Hematopoietic 1 11.5
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1 change: 0 additions & 1 deletion besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt
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Expand Up @@ -3,7 +3,6 @@ Fibroblast Genes used for automatic annotation of scRNA-seq derived clusters of
Endothelial Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS CDH5 ECSCR CCL14 KDR TIE1 PCAT19 MYCT1 FLT4
Epithelial Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS EPCAM KLK1 SMIM22 LGALS4 CLDN7 CDH1 HMGCS2 SERPINB5
Granulocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS MPO CTSG FCGR3B CLC HDC
Malignant Malignant cell signature (harmonized): merged from the former MelMelanoma and ColorectalCancer signatures following nomenclature harmonization (besca PRs #388/#389). MIA TYR SLC45A2 CDH19 PMEL SLC24A5 MAGEA6 GJB1 PLP1 PRAME CAPN3 ERBB3 GPM6B S100B PAX3 S100A1 MLANA S100P CEACAM6 DPEP1 MAL2 REG4
MemBcell Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. TNFRSF13B AIM2 IGHG1 IGHG2 CLECL1 IGHA1
Myeloid Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS CSF3R MS4A6A MS4A7 MNDA C5AR1 FCGR2A C3AR1 FPR1 LILRB2 HDC FCGR3B CCL22
NKcell Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS NCR1 LIM2 KIR2DL4 KLRC1 IL18RAP KLRF1
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1 change: 0 additions & 1 deletion besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,6 @@ Fibroblast Genes used for automatic annotation of scRNA-seq derived clusters of
Endothelial Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Tie1 Cyrr1 Mmrn2 Sox18 Gpr182 Sox17 Myct1 Cldn5 Gpihbp1 Arhgef15
Epithelial Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Sftpd Pigr Scgb3a1 Hmgcs2 Lgals4 Epcam Cldn7 Smim22 Mal2 Serpinb5
Granulocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Mpo Ctsg Mmp9 Clc Hdc
Malignant Malignant cell signature (harmonized): merged from the former MelMelanoma and ColorectalCancer signatures following nomenclature harmonization (besca PRs #388/#389). Gm21983 Tyr Slc45a2 Cdh19 Pmel Slc24a5 Gjb1 Plp1 Capn3 Erbb3 Gpm6b S100b Pax3 S100a1 Mlana Ceacam2 Dpep1 Mal2 Reg4 Gm40318
MemBcell Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Tnfrsf13b Aim2 Igha Ighg1 Ighg2a Ighg2b Ighg2c
Myeloid Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Clec4a3 Clec4a1 Fcgr1 Lst1 Fcgr2b Ms4a6d Cfp Clec5a Mcemp1 Cpa3 Clec4e C5ar1 Chil3 Flt3 Batf3
NKcell Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Ncr1 Klri2 Klrb1a Klra9
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