Update CellNames_scseqCMs6_sigs.gmt

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													

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														

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														

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