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Harmonize CellNames_scseqCMs6 signatures with malignant nomenclature … #390

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Merged
hatjek merged 1 commit into from
Jun 26, 2026
Merged

Harmonize CellNames_scseqCMs6 signatures with malignant nomenclature … #390

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7 changes: 3 additions & 4 deletions besca/datasets/genesets/CellNames_scseqCMs6_config.mouse.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ Fibroblast None 2.75 2
Endothelial None 2.5 3
Epithelial None 2.5 4
Granulocyte Myeloid 0.1 21
MelMelanoma None 2.5 60
Malignant None 2.5 60
MemBcell Bcell 1.5 8
Myeloid Hematopoietic 0.5 12.5
NKcell Hematopoietic 1.5 10.2
Expand Down Expand Up @@ -99,7 +99,6 @@ ActTcell Tcell 2 106
NaiTcell Tcell 1 107
McellGut Epithelial 2 60.9
Mast Myeloid 1.5 10.5
ColorectalCancer None 2 110
T1Pneumocyte Pneumocyte 2 111
T2Pneumocyte Pneumocyte 2 112
Pneumocyte Epithelial 1.5 113
Expand All @@ -122,7 +121,7 @@ cDC_CD209 cDC 1 30.5
Th17CD4Tcell CD4Tcell 2 20.5
Eosinophil Granulocyte 1 82.5
ResourceCD8Tcell CD8Tcell 4 120
Microglia Macrophage 1 121
Microglial Macrophage 1 121
MAIT Tcell 1 122
Keratinocyte Epithelial 2 11
Melanocyte None 2 71
Melanocyte None 2 71
5 changes: 2 additions & 3 deletions besca/datasets/genesets/CellNames_scseqCMs6_config.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ Fibroblast None 3 2
Endothelial None 2 3
Epithelial None 1.75 4
Granulocyte Myeloid 0.05 21
MelMelanoma None 2 60
Malignant None 2 60
MemBcell Bcell 1.5 8
Myeloid Hematopoietic 0.5 12.5
NKcell Hematopoietic 1 11.5
Expand Down Expand Up @@ -99,7 +99,6 @@ ActTcell Tcell 2 106
NaiTcell Tcell 0.75 107
McellGut Epithelial 2 60.9
Mast Myeloid 4 10.5
ColorectalCancer None 2 110
T1Pneumocyte Pneumocyte 2 111
T2Pneumocyte Pneumocyte 2 112
Pneumocyte Epithelial 1.5 113
Expand All @@ -120,7 +119,7 @@ PancreaticEndocrine Enteroendocrine 2 116
ProlifHematopoietic Hematopoietic 2.5 115
Th17CD4Tcell CD4Tcell 4 20.5
Eosinophil Granulocyte 1 82.5
Microglia Macrophage 1 121
Microglial Macrophage 1 121
ResourceCD8Tcell CD8Tcell 4 120
MAIT Tcell 2 13.5
Keratinocyte Epithelial 2 11
Expand Down
7 changes: 3 additions & 4 deletions besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt
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Expand Up @@ -3,7 +3,7 @@ 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
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
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
Expand Down Expand Up @@ -98,7 +98,6 @@ ActTcell Genes used for automatic annotation of scRNA-seq derived clusters of In
NaiTcell Genes used for automatic annotation of scRNA-seq derived clusters of Intestine (v8 May20) derived by Hatje K. Updated in v9 Sep21 TCF7 LEF1 NELL2 CAMK4 MAL TRABD2A
McellGut Genes used for automatic annotation of scRNA-seq derived clusters of Intestine (v8 May20) derived by Hatje K. NTRK2 MIA ICAM2 TNFAIP2 LTB
Mast Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS TPSAB1 CPA3 HPGDS VWA5A
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
T1Pneumocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. AGER CLIC5 SEMA3B
T2Pneumocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. ABCA3 PGC NAPSA SFTPD SFTA2
Pneumocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. ABCA3 PGC AGER NAPSA SPTB CFTR
Expand All @@ -119,8 +118,8 @@ PancreaticEndocrine Genes used for automatic annotation of scRNA-seq derived clu
ProlifHematopoietic Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v8 May20) derived by Schwalie P. MKI67 PCNA STMN1 CKS1B
Th17CD4Tcell Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS IL17A IL17RE RORC IL23R
Eosinophil "Genes derived from literature and expression checked in tested in several datasets. To be further tested and validated. Derived by Alberti Ll, Sep21" CLC PRG2 EPX RNASE3 RNASE2 CD24 SIGLEC8 FUT9 CCR3
Microglia Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS P2RY12 SIGLEC8 TMEM119
Microglial Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS P2RY12 SIGLEC8 TMEM119
ResourceCD8Tcell "Genes derived from literature and expression checked in tested in a single mouse dataset. To be further tested and validated. Derived by PCS, Sep21" S1PR5 KLRG1 SLAMF6 CXCR3 S1PR1 ITGB7 CD8A IL7R TCF7 PDCD1
MAIT Genes derived from literature and DGE analysis of MAIT cells in WB_Glofit study annotated with reference atlas. Derived by LAS Oct21 CD8A KLRB1 CXCR6 CCR6 SLC4A10 LTK
Keratinocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (Mar23) derived by PCS LGALS7 LGALS7B DSC3 DSG1 LY6D FAM83B SERPINB5
Melanocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (Mar23) derived by PCS MLANA DCT TYRP1 PMEL TRPM1 GPR143 TYR
Melanocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (Mar23) derived by PCS MLANA DCT TYRP1 PMEL TRPM1 GPR143 TYR
7 changes: 3 additions & 4 deletions 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 +3,7 @@ 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
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
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
Expand Down Expand Up @@ -98,7 +98,6 @@ ActTcell Genes used for automatic annotation of scRNA-seq derived clusters of PB
NaiTcell Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Tcf7 Lef1 Nsg2 Cd40lg
McellGut Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Ntrk2 Gm21983 Icam2 Tnfaip2 Ltb
Mast Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Tpsab1 Cpa3 Hpgds Vwa5a Mcpt4 Ms4a2
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
T1Pneumocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Ager Clic5 Sema3b
T2Pneumocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Abca3 Pgc Napsa Sftpd Sfta2
Pneumocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Abca3 Pgc Ager Napsa Sptb Cftr
Expand All @@ -121,7 +120,7 @@ cDC_CD209 Genes used for automatic annotation of scRNA-seq derived clusters of P
Th17CD4Tcell Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Cd163l1 Il17a Kcnc1 Il17re Il23r Rorc Prr29
Eosinophil "Genes derived from human homology and literature. To be further tested and validated. Derived by Alberti Ll, Sep21" Prg2 Epx Ear6 Fut9 Ccr3
ResourceCD8Tcell Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Tcf7 Pdcd1 Cd8b1 S1pr5 S1pr1 Ly6c2 Cxcr3 Slamf6 Ccr2 Itgb7 Il7r
Microglia Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Gpr84 Mertk Gpr34 Trem2
Microglial Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (v9 Sep21) derived by LAS and PCS Gpr84 Mertk Gpr34 Trem2
MAIT Genes derived from literature and DGE analysis of MAIT cells in WB_Glofit study annotated with reference atlas. Derived by LAS Oct21. Needs more testing in mouse datasets Cd8a Klrb1 Cxcr6 Ccr6 Slc4a10 Ltk
Keratinocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (Mar23) derived by PCS in human, needs testing in mouse datasets Lgals7 Dsc3 Dsg1a Ly6d Fam83b Serpinb5
Melanocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (Mar23) derived by PCS in human, needs testing in mouse datasets Mlana Dct Tyrp1 Pmel Cdk2 Gpr143 Trpm1 Tyr
Melanocyte Genes used for automatic annotation of scRNA-seq derived clusters of PBMCs/TILs (Mar23) derived by PCS in human, needs testing in mouse datasets Mlana Dct Tyrp1 Pmel Cdk2 Gpr143 Trpm1 Tyr
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