diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_config.mouse.tsv b/besca/datasets/genesets/CellNames_scseqCMs6_config.mouse.tsv index 57985135..261ed1e3 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_config.mouse.tsv +++ b/besca/datasets/genesets/CellNames_scseqCMs6_config.mouse.tsv @@ -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 @@ -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 @@ -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 \ No newline at end of file +Melanocyte None 2 71 diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_config.tsv b/besca/datasets/genesets/CellNames_scseqCMs6_config.tsv index 6fd0d9aa..4dcd4f66 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_config.tsv +++ b/besca/datasets/genesets/CellNames_scseqCMs6_config.tsv @@ -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 @@ -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 @@ -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 diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt b/besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt index 97600704..d3215e30 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt +++ b/besca/datasets/genesets/CellNames_scseqCMs6_sigs.gmt @@ -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 @@ -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 @@ -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 \ No newline at end of file +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 diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt b/besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt index c6a4651e..184d0355 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt +++ b/besca/datasets/genesets/CellNames_scseqCMs6_sigs.mouse.gmt @@ -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 @@ -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 @@ -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 \ No newline at end of file +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