diff --git a/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt b/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt index 0f5f3bdb..5b022a80 100644 --- a/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt +++ b/besca/datasets/genesets/CellNames_scseqCMs6_Extrasigs.gmt @@ -30,7 +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 +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 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 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 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