TABLE 13B: Alternative Gene Set for DNA methylation gene set or Gene Expression  or lineage marker propensity differentiation assay (small Subgroup)																																																																																																																																																																																																																																																															
																																																																																																																																																																																																																																																															
"All categories (363 genes included, 1042 genes excluded)"																																																																																																																																																																																																																																																															
Included:	ABCB1	ABCG2	ACAN	ACE	ACTA1	ACTA2	ACTB	ACTN1	ADIPOQ	AFP	ALB	ALPL	ALX1	ANPEP	APOA1	APOA2	APOE	BCL10	BCL2	BDNF	BGLAP	BGN	BMI1	BMP2	BMP4	BMPER	BMPR1A	BRCA1	CACNA1H	CALCB	CAMK2A	CAPN1	CARTPT	CAT	CD14	CD151	CD19	CD22	CD24	CD28	CD34	CD36	CD3E	CD4	CD40	CD44	CD46	CD59	CD8A	CD9	CDCP1	CDH1	CDH15	CDH2	CDH5	CDKN2A	CDKN2B	CDX2	CEACAM1	CEACAM5	CEBPB	CEBPG	CHRNA7	CHUK	CNTF	COL17A1	COL1A1	COL2A1	COL3A1	COL4A2	COL4A4	COMP	COMT	CRABP2	CRCT1	CREBBP	CRTAC1	CSF1R	CTNNB1	CXCR4	CYP2E1	DCN	DDX3X	DDX3Y	DES	DLK1	DLL1	DLX5	DMD	DMP1	DNMT3B	E2F1	EBF1	EGF	EGFR	ELF3	EN1	ENG	ENO3	EOMES	EP300	EPCAM	EPHB2	EPHB4	EPO	EPYC	ERAS	ERBB2	ERCC2	EREG	ERG	ETV2	FABP1	FABP2	FABP3	FABP4	FAM24B	FAS	FASLG	FBXW7	FCGR3A	FCGR3B	FGB	FGF10	FGF2	FGF7	FGF8	FGFR2	FGFR3	FGG	FMO3	FMOD	FN1	FOS	FOXA1	FOXA2	FOXD3	FUT4	GAS6	GATA1	GATA2	GATA3	GATA4	GATA6	GCG	GDF10	GDNF	GFAP	GLI2	GLMN	GNL3	GREM1	GSC	GSK3B	HAND1	HHEX	HIST1H3C	HLA-DRA	HMGA2	HNF1A	HNF1B	HNF4A	HOXA1	HOXA5	HOXA9	HOXB4	HOXC4	HOXC9	HRAS	HTATSF1	HTRA4	ICAM1	IFNGR1	IGFBP3	IL12B	IL4	IL8	INHBA	INS	IRF6	ISL1	ISL2	ITGA2B	ITGA4	ITGA6	ITGAL	ITGAM	ITGAV	ITGAX	ITGB1	ITGB2	ITGB3	JAG1	JMJD6	JUN	KDR	KIT	KLF4	KLF6	KRT1	KRT14	KRT5	KRT8	LAMA1	LAMB1	LAMC1	LEF1	LEFTY1	LEFTY2	LIN28	LMX1A	LPL	LRP2	MAP2	MAP2K1	MAP3K1	MAPK1	MAPK14	MAPK3	MAPK8	MAPT	MCAM	MEF2C	MEG3	MKL1	MME	MMP1	MNX1	MOS	MPL	MSI1	MSX1	MYC	MYF5	MYH3	MYL2	MYOD1	MYOG	NANOG	NCAM1	NEFL	NES	NEUROD1	NEUROG1	NEUROG3	NFKB1	NFKBIA	NGFR	NKX2-2	NKX2-5	NKX6-1	NME1	NME2	NODAL	NOG
Excluded:	ABCA4	ABCB10	ABCB7	ABCC2	ACHE	ACIN1	ACO1	ACPP	ACTC1	ACTG1	ACVR1	ACVR1B	ACVR2A	ACVRL1	ADAM12	ADAMTS13	AEBP1	AGBL2	AGGF1	AGR2	AHCTF1	AHSA1	AHSG	AKAP12	AKR1C4	ALAS2	ALCAM	ALDH1A1	ALDH3A2	ALMS1	ALOX12B	ALOX15	ALPK3	ALS2	AMH	AMIGO1	AMOT	ANG	ANGPTL2	ANGPTL3	ANGPTL4	ANKH	ANXA1	ANXA6	APBB1	APOB	APOF	AQP4	AR	AREG	AREGB	ARG1	ARHGEF15	ARID1A	ARID3B	ARSA	ARTN	ARX	ASB3	ASCL1	ASPSCR1	ATP2A2	ATP2A3	ATP2B2	ATP2C1	ATP6V0A4	ATP6V1B1	ATPIF1	ATXN1	AZU1	B3GALT5	B3GAT1	B3GNTL1	BAI1	BAIAP2	BARX1	BIK	BMP10	BMP7	BMP8B	BMPR1B	BMPR2	BNC1	BOC	BRSK2	BSG	BST1	BST2	BTD	BTG1	BTG4	BXDC2	C10orf137	C12orf56	C16ORF80	C1GALT1	C1ORF77	C4BPB	C8A	CACNA1C	CACNB2	CALCA	CALCRL	CALML5	CAMK2B	CAMK2D	CAMK2G	CAMK4	CANX	CAPN3	CASP10	CASP14	CASQ2	CASR	CAV2	CAV3	CCDC11	CCDC80	CCKBR	CCL11	CCL27	CCM2	CCR2	CCR4	CCR5	CD109	CD164	CD1A	CD1B	CD1C	CD1D	CD1E	CD2	CD209	CD244	CD247	CD27	CD276	CD33	CD37	CD38	CD3D	CD3G	CD48	CD5	CD55	CD6	CD69	CD7	CD70	CD72	CD79A	CD80	CD81	CD82	CD84	CD86	CD8B	CD93	CD96	CD97	CDC27	CDC42	CDCA4	CDH13	CDH3	CDK5	CDK5R1	CDK6	CDSN	CDX4	CEACAM6	CEBPA	CELSR1	CENPF	CENTA2	CEP152	CER1	CFDP1	CFTR	CGB	CH25H	CHAT	CHI3L2	CHRD	CHRDL1	CHRM3	CHRNA1	CHRNE	CIB2	CIDEA	CIT	CITED2	CLCN1	CLDN1	CLDN3	CLDN4	CLDN6	CLEC9A	CLN5	CNN1	CNN2	CNTN1	CNTN4	COL10A1	COL13A1	COL1A2	COL4A3	COL4A6	COL5A2	COL5A3	COL6A3	COL7A1	COMMD3	CP	CPA1	CPA2	CPA3	CPN1	CPN2	CR1	CR1L	CR2	CRP	CRYGA	CRYGD	CSF1	CSF2	CSF2RA	CSF3	CSF3R	CSNK1E	CSNK2A1	CSNK2B	CSPG5	CSRP1	CSRP3	CST1	CST3	CSTA	CTDSPL	CTF1	CTGF	CTH	CTLA4	CTNNA1	CTNND1	CTNND2	CUL7	CX3CL1	CXCL10	CXCL12	CYFIP1	CYP1A1	CYP3A7

"Ectoderm germ layer (51 genes included, 37 genes excluded)"																																																																																																																																																																																																																																																															
Included:	ABCB1	ABCG2	APOE	CD24	CD44	CDH2	CRABP2	CXCR4	EN1	FAS	FGFR2	FN1	FUT4	GATA2	GATA3	GFAP	HAND1	ICAM1	ITGA4	ITGA6	ITGB1	JAG1	MAP2	MAPT	MCAM	MNX1	NCAM1	NEFL	NES	NEUROG3	NGFR	NOG	NOTCH1	OTX2	PAX3	PAX5	PAX6	PAX7	PDGFRA	S100B	SNAI2	SOX10	SOX2	SOX9	SYP	SYT1	TDGF1	TH	THY1	TP63	VIM																																																																																																																																																																																																												
Excluded:	AGR2	B3GAT1	CD81	CHAT	CHRD	CNTN1	CSPG5	DCX	DLG4	EDA	ENO2	GABRA1	GAD2	GAP43	GCM2	GLUL	GRIA2	GRID2	GRIK1	GRM1	INA	LHX1	LHX3	MKI67	NCSTN	NEFH	NEFM	NRP2	NTRK2	PIK3R4	PVRL2	SMN1	SNCA	STX1A	SYN1	TUB	ZEB2																																																																																																																																																																																																																										

"Mesoderm germ layer (87 genes included, 61 genes excluded)"																																																																																																																																																																																																																																																															
Included:	ABCB1	ABCG2	ACTA2	ACTB	ACTN1	ADIPOQ	ANPEP	BMP2	CAPN1	CD14	CD151	CD19	CD24	CD34	CD36	CD4	CD44	CD59	CD9	CDCP1	CDH1	CDH15	CDH2	CDH5	CEACAM1	CSF1R	CXCR4	DES	DLL1	ENG	ENO3	FABP4	FCGR3A	FCGR3B	FN1	FOXA2	FUT4	GATA3	GATA4	GSC	HAND1	HHEX	HLA-DRA	ICAM1	IGFBP3	INHBA	ITGA2B	ITGA4	ITGA6	ITGAL	ITGAM	ITGAV	ITGAX	ITGB1	ITGB2	ITGB3	KDR	KIT	LEF1	MCAM	MME	MYH3	MYOD1	MYOG	NCAM1	NES	NGFR	NODAL	NOTCH1	PECAM1	PTPRC	SDC1	SPI1	SRF	STAT3	T	TAZ	TFRC	TGFB1	THBD	THY1	TNFRSF1A	TNFRSF1B	TNNI3	TWIST1	VCAM1	VIM																																																																																																																																																																								
Excluded:	ALCAM	ANXA6	BSG	BST1	CAMK4	CAV2	CAV3	CCR2	CD109	CD164	CD2	CD209	CD33	CD38	CD48	CD55	CD79A	CD84	CD93	CD97	CEACAM6	CSF2RA	CSF3	CSF3R	CTLA4	CXCL10	DNTT	FGF5	GJA1	GPC3	HES7	HFE2	HIF1A	ICAM2	IL1R1	IL32	IL4R	IL7R	ITGA5	LRP1	MEOX1	MESDC2	MIXL1	MS4A1	MSH3	NFYA	NT5E	OSR1	PROCR	PVRL2	SELE	SELL	SELP	TEK	TIE1	TNFRSF10B	TNFSF10	TNFSF4	WAS	WNT3A	WNT8A																																																																																																																																																																																																		

"Endoderm germ layer (36 genes included, 14 genes excluded)"																																																																																																																																																																																																																																																															
Included:	ALB	APOE	CD44	CDCP1	CDH2	CDX2	CTNNB1	CXCR4	DLX5	FABP1	FABP2	FOXA1	FOXA2	GATA3	GATA4	GATA6	GCG	HNF1A	HNF1B	HTATSF1	ISL1	ITGA6	ITGB1	LRP2	NEUROG3	NKX2-5	PAX6	PDX1	SLC2A2	SOX17	SOX7	SPARC	SST	SYP	THY1	VIM																																																																																																																																																																																																																											
Excluded:	CLDN6	DLX3	FGF23	FOXG1	GAD2	ID4	MIXL1	NPNT	NRP2	PAX9	RAB15	RIPK4	STRA6	TMPRSS2																																																																																																																																																		

"Pluripotent cell signature (59 genes included, 69 genes excluded)"																																																																																																																																																																
Included:	ABCG2	ALPL	CAMK2A	CD24	CD9	CDH1	CDKN2A	CDX2	CREBBP	CTNNB1	DDX3X	DLL1	E2F1	EP300	EPCAM	EPHB2	ERAS	FGF10	FGF2	FOXD3	FUT4	GNL3	GREM1	GSK3B	IFNGR1	IRF6	ITGA6	ITGB1	JAG1	JMJD6	KIT	KLF4	LIN28	MAP2K1	MAPK1	MAPK3	MYC	NANOG	NEUROG3	NODAL	NOTCH1	PODXL	POU5F1	PROM1	RAF1	ROCK1	SHH	SOX17	SOX2	SP1	STAT1	STAT3	STAT5A	TDGF1	TERT	TGIF1	UTF1	ZFP42	ZFX																																																																																																					
Excluded:	AHSA1	ARID3B	B3GALT5	BMPR2	CCR4	CSNK1E	CSNK2A1	CSNK2B	CTNNA1	CTNND1	DDIT3	DDX4	DPPA4	DPPA5	DZIP1	E2F2	E2F3	EHMT2	FZD5	GDF3	GREM2	HDAC3	HESX1	HMMR	HOXB8	HOXC13	HOXD8	ID1	ID2	ID3	IL6ST	KITLG	KRT7	LRIG3	MAP2K2	MAPK6	MELK	NACC1	NCSTN	NR5A2	NR6A1	PUM2	RBL1	ROCK2	SALL4	SGK1	SHB	SIPA1	SMAD2	SMAD4	SNX6	ST3GAL3	STAT4	STAT6	STRA8	TACSTD2	TFCP2L1	TFDP1	TNFRSF8	WNT16	YBX1	YWHAQ	ZFP57	ZIC3	ZMYM2	ZNF219	ZNF281	ZNF323	ZSCAN10																																																																																											

"Male/female classification (5 genes included, 0 genes excluded)"																																																																																																																																																																
Included:	DDX3X	DDX3Y	RPS4Y1	SRY	XIST																																																																																																																																																											
Excluded:																																																																																																																																																																

"Neural lineage (92 genes included, 160 genes excluded)"																																																																																																																																																																
Included:	ABCB1	ABCG2	APOE	BMP2	BMP4	CAMK2A	CD24	CD34	CDH2	CEACAM1	CEACAM5	CNTF	CXCR4	DLK1	DLL1	DLX5	EN1	EOMES	EPHB4	FAS	FCGR3A	FCGR3B	FGF2	FGF8	FGFR2	FGFR3	FN1	FOXD3	FUT4	GDNF	GFAP	GLI2	GNL3	HMGA2	ICAM1	ISL1	ISL2	ITGA4	ITGA6	ITGAM	ITGB1	JAG1	LAMB1	LIN28	LMX1A	MAP2	MAPT	MCAM	MEF2C	MNX1	MSI1	MSX1	NCAM1	NEFL	NES	NEUROD1	NEUROG1	NGFR	NKX2-5	NOG	NOTCH1	NR2E1	OLIG2	OTX2	PAX3	PAX5	PAX6	POU5F1	PROM1	PTPRC	RUNX1	S100B	SDC1	SHH	SNAI2	SOX1	SOX10	SOX2	SOX4	SOX9	SYP	SYT1	TCF3	TCF4	TFRC	TGFB2	TGIF1	TH	THY1	TUBB3	TWIST1	VIM																																																																				
Excluded:	ALDH1A1	ALS2	AMIGO1	ARTN	ASCL1	ATP2B2	AZU1	BAI1	BAIAP2	BARX1	BRSK2	BTG4	CAMK2B	CAMK2D	CAMK2G	CD81	CDK5	CDK5R1	CDK6	CHAT	CHRD	CHRDL1	CIT	CLN5	CNTN1	CNTN4	CSPG5	CST3	CTNND2	CYFIP1	DBX2	DCX	DGCR6	DLG4	DLX1	DLX2	DPYSL5	DTX1	EIF2B1	EIF2B2	EIF2B3	EIF2B4	EIF2B5	ELAVL4	EMX1	ENO2	ETV1	EYA3	FABP7	FARP2	FEZ1	FEZ2	FGFR4	FZD9	GABRA1	GAD2	GAP43	GDF7	GHRL	GLUL	GRIA2	GRID2	GRIK1	GRM1	GSX1	HAS3	HES5	HFE2	IPMK	KAL1	KCNIP2	KLK8	KRT2	LAMP1	LBX1	LDB1	LHX1	LHX2	LLGL1	LMX1B	LRRC4C	LST1	MAP1S	MDGA1	MKI67	MSI2	NCSTN	NEDD1	NEFH	NEFM	NEUROD2	NF1	NF2	NGF	NLGN1	NOTCH2	NOTCH3	NPTN	NRCAM	NRP1	NRP2	NRTN	NRXN1	NRXN3	NTNG1	NTNG2	NTRK2	OLFM1	OPHN1	PARD3	PARD6B	PAX2	PCSK9	PICK1	PIK3R4	PLAGL1	POU4F1	POU6F2	PPT1	PVRL2	RACGAP1	RND1	ROBO1	ROBO2	RTN1	RTN4	RTN4RL1	RTN4RL2	SEMA3B	SEMA4F	SERPINF1	SIAH1	SIGLEC7	SLC1A3	SLC2A1	SLIT1	SLIT2	SMARCA1	SMARCA4	SMN1	SNCA	SOD1	SOX11	SOX12	SPON2	STX1A	SYN1	TAGLN3	TBX6	TMEM176B	TNC	TRAPPC4	TSPAN2	TUB	UBB	UNC5C	VWC2	YWHAG	YWHAH	ZEB2

"Hematopoietic lineage (89 genes included, 168 genes excluded)"																																																																																																																																																																
Included:	ABCB1	ABCG2	ACE	ALB	ANPEP	BMI1	BMPR1A	CD14	CD19	CD22	CD24	CD28	CD34	CD36	CD3E	CD4	CD40	CD44	CD59	CD8A	CD9	CDCP1	CDH1	CDH2	CDH5	CEACAM1	CEACAM5	CSF1R	CXCR4	DLK1	DLL1	EBF1	ENG	EPHB4	EPO	ERG	ETV2	FAS	FASLG	FCGR3A	FCGR3B	FUT4	GAS6	GATA1	GATA2	GATA3	HLA-DRA	HOXB4	ICAM1	IFNGR1	IL4	IRF6	ITGA2B	ITGA4	ITGA6	ITGAL	ITGAM	ITGAV	ITGAX	ITGB2	ITGB3	JAG1	JMJD6	KDR	KIT	KLF6	MME	MPL	NCAM1	NOTCH1	PECAM1	PODXL	PROM1	PTPRC	RUNX1	SDC1	SPEN	T	TAL1	TFRC	THBD	THPO	THY1	TNF	TNFRSF1A	VCAM1	VNN1	ZBTB16	ZFX																																																																							
Excluded:	ABCB7	AHCTF1	ALDH1A1	ANGPTL2	ATXN1	BST2	C10orf137	CAMK4	CD164	CD1A	CD1B	CD1C	CD1D	CD1E	CD2	CD244	CD247	CD27	CD276	CD33	CD37	CD38	CD3D	CD3G	CD48	CD5	CD55	CD6	CD69	CD7	CD70	CD72	CD79A	CD80	CD84	CD86	CD8B	CD93	CD96	CD97	CDCA4	CDX4	CLEC9A	CPA3	CR1	CR2	CSF1	CSF2	CSF2RA	CSF3	CSF3R	CTLA4	DLX1	DNTT	DPP4	DYRK3	ENPEP	EPOR	EPX	ERMAP	ETV1	FAIM2	FCER2	FCGR1A	FCGR2A	FCGR2B	FCGR2C	FLT3	FLT3LG	FLVCR1	FSTL3	GCNT2	GIMAP4	GNA15	GP1BA	GP1BB	GP5	GP9	GYPA	HAS3	HBS1L	HEMGN	HFE	HLA-DRB1	HLA-DRB3	HLA-DRB4	HLA-DRB5	HOXB3	ICAM2	IGHD	IGHM	IL11	IL11RA	IL1A	IL1B	IL1R1	IL1R2	IL1RN	IL2RA	IL2RB	IL3	IL32	IL3RA	IL4R	IL5	IL5RA	IL6	IL6R	IL7	IL7R	IL9R	IRGM	ITGA1	ITGA2	ITGA3	ITGA5	ITGAE	ITGB7	JAG2	KITLG	KRT7	LAMP1	LAMP2	LHX2	LMO2	LXN	MAEA	MEIS1	MLF1	MLL5	MNDA	MS4A1	MSH3	NCR3	NFYA	NMT1	NOTCH3	PBX1	PCGF2	PHC1	PIM1	PIWIL1	PRNP	PROCR	SAMSN1	SELL	SELP	SIGLEC7	SLAMF1	SLC3A2	SOCS3	SPN	TBX21	TEK	TMEM176B	TNFRSF4	TNFRSF9	TPO	TRA@	TRIB1	TRIB2	TRIM22	TRIM33	USE1	VNN2	VPREB3	VWF	WAS

"Epidermis (38 genes included, 86 genes excluded)"																																																																																																																																																																								
Included:	BCL2	CHUK	COL17A1	COL1A1	CRABP2	EGF	EGFR	ERCC2	EREG	FGF7	FOS	HRAS	ITGA6	JUN	KRT1	KRT14	KRT5	MAP2K1	MAP3K1	MAPK1	MAPK14	MAPK3	MAPK8	NFKB1	NFKBIA	NME2	PRKCA	PRKCB1	RAF1	RELA	SP1	SPINK5	TFRC	TGFB2	TNF	TNFRSF1A	TNFRSF1B	TRAF2																																																																																																																																		
Excluded:	ALDH3A2	ALOX12B	ANXA1	ATP2A2	ATP2C1	BNC1	BTD	CALML5	CASP14	CDSN	CEBPA	COL5A2	COL7A1	CSTA	CTGF	DAXX	DCT	DHCR24	DSP	EMP1	ERCC3	ETS1	ETS2	EVPL	FABP5	FLOT2	FOXN1	FST	GJB5	GLI1	HOXA7	HOXB13	IKBKB	IL20	IVL	KLK5	KLK7	KRT10	KRT13	KRT15	KRT16	KRT17	KRT2	KRT31	KRT32	KRT34	KRT83	KRT85	KRT9	KRTAP5-9	LAMA3	LAMB3	LAMC2	LOR	MAP2K3	MAP2K4	MAP2K6	MAP2K7	MAP3K14	MAP3K5	MAPK13	PLOD1	POU2F3	PPARD	PPP2CA	PRKCD	PRKCE	PRKCG	PRKCH	PRKCQ	PTCH2	PTHLH	RBP2	RIPK1	S100A7	SASP	SCEL	SPRR1A	SPRR1B	STS	TGM1	TGM3	TGM5	TXNIP	UGCG	WAS																																																																																		

"Mesenchymal stem cell (70 genes included, 47 genes excluded)"																																																																																																																																																																								
Included:	ACAN	ACTA2	ADIPOQ	ALPL	ALX1	ANPEP	BGLAP	BGN	BMP2	BMPER	BMPR1A	CD14	CD34	CD3E	CD44	CEACAM1	CEACAM5	COL1A1	COL2A1	COL3A1	COL4A2	COL4A4	COMP	CRTAC1	CSF1R	DCN	DES	DMD	DMP1	ENG	FABP3	FABP4	FCGR3A	FCGR3B	FGF8	FMOD	FN1	FUT4	GAS6	GATA4	GDF10	GLMN	GNL3	ITGAM	ITGB1	KIT	LPL	MEF2C	MKL1	MME	MYF5	MYL2	MYOG	NGFR	NKX2-5	PAX3	PAX7	PECAM1	PPARG	RUNX2	SCXA	SIX2	SOX9	SP7	SPARC	THPO	TNFRSF1A	TNNT2	VCAM1	VNN1																																																																																																		
Excluded:	ACTG1	ASPSCR1	BMP8B	BMPR1B	BMPR2	BOC	CCDC80	CFDP1	CHI3L2	CNN1	COL1A2	CSF2RA	CYR61	DBX2	FAM65B	FBXO32	FLII	FNDC3B	FSTL3	IBSP	ICAM2	ITGA1	ITGB1BP3	KLF5	LBX1	LEP	MESDC2	MTM1	MYOM2	NOC3L	OSTN	PAMR1	PDGFC	PTHLH	ROR2	SFRP2	SLC2A4	SPP1	SPRY2	SRPK3	STC2	TAGLN3	TNC	TWIST2	WISP2	WISP3	WWTR1																																																																																																																									

"Bone (21 genes included, 32 genes excluded)"																																																																																																																																																																								
Included:	ALPL	ALX1	BGLAP	BGN	BMP2	BMP4	CARTPT	COL1A1	COL3A1	DCN	DMP1	FN1	GDF10	GLI2	IGFBP3	MSX1	RUNX2	SOX9	SP7	SPARC	THPO																																																																																																																																																			
Excluded:	ACHE	ACVR1	AHSG	ANKH	ATP6V0A4	ATP6V1B1	CALCA	CASR	CCDC80	CDK6	CFDP1	COL13A1	COL1A2	DSPP	FSTL3	GLI1	IBSP	IL7	KL	MC4R	MEPE	MGP	NF1	OSTF1	OSTN	ROR2	SPP1	STATH	TPO	TPP1	TWIST2	ZNF675																																																																																																																																								

"Cartilage (21 genes included, 2 genes excluded)"																																																																																																																																																																								
Included:	ACAN	ALX1	BMP2	BMPER	CD151	CD44	COL2A1	COL3A1	COL4A2	COL4A4	COMP	CRTAC1	DMP1	EPYC	FMOD	GAS6	GDF10	SCXA	SIX2	SOX9	VNN1																																																																																																																																																			
Excluded:	CFDP1	CHI3L2																																																																																								

"Fat (21 genes included, 20 genes excluded)"																																																																																										
Included:	ADIPOQ	BMPR1A	CD34	CEBPB	CEBPG	DLK1	EN1	FABP2	FABP3	FABP4	HOXA1	HOXA5	HOXC4	HOXC9	LPL	LRP2	NR2F1	PECAM1	PPARG	PPARGC1A	THBD																																																																					
Excluded:	ASPSCR1	CCDC80	CEBPA	CIDEA	DIO2	ELOVL3	FNDC3B	FOXC2	HOXA4	LEP	NOC3L	PAPPA	PCSK9	PPARA	PRDM16	SFRP1	SHOX2	SLC2A4	TCF21	UCP1																																																																						

"Muscle (40 genes included, 90 genes excluded)"																																																																																										
Included:	ACTA1	ACTA2	ACTB	ACTN1	BMP4	CACNA1H	CAPN1	CDH15	CDH2	COL4A4	DES	DMD	ENO3	EREG	FABP3	FGF8	GATA4	GATA6	GLMN	IGFBP3	MCAM	MEF2C	MKL1	MYF5	MYH3	MYL2	MYOD1	MYOG	NKX2-5	NOTCH1	PAX3	PAX7	SOX10	TAZ	TBX3	TGFB1	TNNI3	TNNT2	TWIST1	VIM																																																		
Excluded:	ACHE	ACTG1	ADAM12	AEBP1	BOC	CACNB2	CAPN3	CENPF	CHRNA1	CNN1	CNN2	COL5A3	COL6A3	CSRP3	CTF1	CXCL10	EGR2	EGR3	EMD	EVC	FAM65B	FBXO32	FHL3	FOXL2	GAA	GYLTL1B	HBEGF	HDAC4	HDAC5	HDAC7A	HDAC9	IFRD1	IGF1	ITGA11	ITGA7	ITGB1BP2	ITGB1BP3	KCNH1	KRT19	LAMA2	LARGE	LBX1	MAPK12	MBNL1	MEF2A	MEF2B	MEF2D	MKL2	MKX	MRAS	MTM1	MUSK	MYBPC3	MYEF2	MYF6	MYH11	MYH6	MYH7	MYL3	MYL6	MYL6B	MYOM2	MYOZ1	NF1	NRD1	PAMR1	POU6F1	SFRP2	SGCA	SGCB	SGCD	SGCE	SGCG	SIRT2	SIX1	SMTN	SOD1	SPEG	SRI	SRPK3	SVIL	SYNE1	TAGLN	TAGLN3	TCF12	TEAD4	TTN	UBB	UTRN	VAMP5

"Blood vessel (62 genes included, 76 genes excluded)"																																																																																										
Included:	ACE	ACTA2	BMPER	CD14	CD151	CD34	CD36	CDH2	CDH5	CHRNA7	COL4A2	CSF1R	CXCR4	EGF	ENG	EPHB4	EPO	FCGR3A	FCGR3B	FGF10	FGF2	FGF8	FGFR2	FGFR3	FUT4	GLMN	HOXA9	ICAM1	IL8	INHBA	ITGA2B	ITGA4	ITGA6	ITGAV	ITGB1	ITGB2	ITGB3	JAG1	KDR	KIT	MCAM	MKL1	NCAM1	NES	PECAM1	PF4	PML	PODXL	PTPRC	RUNX1	SHH	SPARC	SPINK5	STAT3	TGFB2	THBD	THY1	TNFRSF1A	TNFRSF1B	TNNI3	VCAM1	VIM																												
Excluded:	ACVRL1	AGGF1	ALCAM	AMOT	ANG	ANGPTL2	ANGPTL3	ANGPTL4	ATPIF1	BSG	BST1	BTG1	C1GALT1	CALCA	CANX	CCM2	CCR2	CD109	CD209	CD93	CDH13	COL4A3	CSF2RA	CTLA4	CUL7	CXCL10	DLG1	EGFL7	EMCN	FGFR4	FOXC2	GHRL	HIF1A	HTATIP2	ICAM2	IL11	IL17F	IL18	IL1R1	IL4R	ITGA5	MYH9	NCL	NF1	NOTCH4	NPPB	NPR1	PDGFC	PDPN	PLG	PPP1R13B	PROCR	PROK2	PVRL2	RASA1	RHOB	RNH1	ROBO4	RTF1	SCG2	SCYE1	SELE	SELL	SELP	SERPINF1	SPHK1	SPRY2	STAB1	TEK	TIE1	TNFRSF10B	TNFSF10	TNFSF12	TNFSF15	TNFSF4	VWF														

"Heart (39 genes included, 47 genes excluded)"																																																																																										
Included:	ACTA1	ACTA2	ACTN1	BMP2	CAMK2A	CD34	CDH15	CDH2	CDH5	CEACAM1	DES	ERBB2	FABP3	FCGR3A	FCGR3B	GATA2	GATA4	GLI2	HAND1	ISL1	KDR	KIT	MEF2C	MKL1	MYH3	MYL2	MYOG	NKX2-5	NOTCH1	PECAM1	SHH	SRF	T	TAZ	TDGF1	TGFB2	TNNI3	TNNT2	VCAM1																																																			
Excluded:	ACTG1	ALCAM	ALPK3	ANXA6	BMP10	BMPR2	CAMK2B	CAMK2D	CAMK2G	CASQ2	CAV2	CAV3	CEACAM6	CENTA2	CITED2	DVL1	DVL3	ECE2	FBN1	FGF12	GJA1	HAND2	HESX1	IRGM	IRX4	KLF5	LAMP2	MKKS	MYBPC3	MYH11	MYH6	MYH7	MYOM2	NCOA6	NF1	NFYA	NKX2-6	OSR1	PLCE1	POU6F1	SHOX2	SLC2A4	SRI	TBX1	TBX5	TEK	VANGL2																										

"Lymphoid cells (42 genes included, 73 genes excluded)"																																																																									
Included:	ANPEP	BMPR1A	CD14	CD19	CD22	CD24	CD28	CD34	CD3E	CD4	CD40	CD44	CD8A	CEACAM1	CEACAM5	CEBPG	FAS	FASLG	FCGR3A	FCGR3B	GATA3	HLA-DRA	ICAM1	IFNGR1	IL12B	IL4	INHBA	ITGAL	ITGAM	ITGAV	ITGAX	ITGB2	KIT	MME	NCAM1	PECAM1	PTPRC	SDC1	SPEN	SPINK5	TFRC	THY1																															
Excluded:	BST2	CD1D	CD2	CD244	CD247	CD27	CD276	CD38	CD3D	CD5	CD6	CD69	CD70	CD72	CD79A	CD80	CD84	CD86	CD8B	CD96	CTLA4	DNTT	DPP4	ENPEP	FAIM2	FCER2	FCGR2A	FCGR2B	FCGR2C	FSTL3	GIMAP4	HDAC4	HDAC5	HDAC7A	HDAC9	HOXB3	ICAM2	IGHD	IGHM	IL11	IL1R1	IL1RN	IL2	IL27	IL2RA	IL2RB	IL4R	IL6R	IL7	IL7R	INHA	ITGAE	ITGB7	JAG2	LAMP1	LCK	MS4A1	NCR3	NFAM1	NHEJ1	SART1	SELL	SLC3A2	SOCS5	SPN	TBX21	TNFRSF4	TNFRSF9	TPD52	TRA@	TRIM22	VPREB3	ZAP70

"Myeloid cells (42 genes included, 69 genes excluded)"																																																																									
Included:	ANPEP	CARTPT	CD14	CD24	CD34	CD36	CD4	CD40	CD44	CD8A	CEACAM1	CEACAM5	CEBPG	CSF1R	ENG	ETV2	FCGR3A	FCGR3B	FUT4	GAS6	HLA-DRA	IFNGR1	IL4	INHBA	ITGA2B	ITGA6	ITGAL	ITGAM	ITGAV	ITGAX	ITGB2	ITGB3	KIT	MPL	PECAM1	PF4	PTPRC	RUNX1	SPI1	TFRC	THY1	ZBTB16																															
Excluded:	ABCB7	ACIN1	ACVR1B	ACVR2A	ALAS2	C10orf137	CALCA	CD1D	CD2	CD33	CD38	CD80	CD86	CD8B	CDC42	CDK6	CPA3	CR1	CSF1	CSF2RA	CSF3R	DYRK3	EPX	ERMAP	ETS1	FCGR2A	FCGR2B	FCGR2C	GCNT2	HBS1L	HCLS1	HFE	IFI16	IL11	IL1R1	IL1RN	IL2RA	IL31RA	IL6R	IL7R	INHA	ITGA5	LAMP1	LAMP2	LDB1	LRP1	LYN	MAEA	MAFB	MEIS1	MMP9	MNDA	MYH9	MYST1	MYST3	NCOA6	NMT1	RASGRP4	RPS19	SCIN	SELL	SELP	SNRK	SPN	TM7SF4	TMEM176B	TRIB1	VNN2	ZNF675				

"Liver (21 genes included, 38 genes excluded)"																																																																									
Included:	AFP	ALB	APOE	CD44	CEBPB	FABP1	FMO3	FOXA2	GATA4	HHEX	HNF1A	HNF1B	HNF4A	HTATSF1	ITGA6	ITGB1	ONECUT1	PROX1	RXRA	TBX3	THY1																																																				
Excluded:	AKR1C4	APOF	ARG1	ARID1A	C4BPB	C8A	CPN1	CPN2	CRP	CRYGA	CTH	CYP3A7	CYP4F11	DDT	DHODH	F12	FLJ34306	G6Pc	GCGR	GCKR	HABP2	HAO1	IGFALS	ITIH2	LECT2	LIPC	LPA	MBL2	MET	RDH16	SEC15L2	SLC22A1	SLC25A20	SLC2A1	SLC6A12	SPP2	TAT	UGT2B4																																			

"Pancreas (22 genes included, 45 genes excluded)"																																																																									
Included:	ERCC2	FOXA2	GCG	HHEX	INS	ISL1	ITGA6	MNX1	NEUROD1	NEUROG3	NKX2-2	NKX6-1	ONECUT1	PAX4	PAX6	PDX1	PML	RUNX2	SLC2A2	SOX9	SST	SYP																																																			
Excluded:	ABCB10	ALMS1	ARHGEF15	ARX	B3GNTL1	C16ORF80	C1ORF77	CCL27	CEP152	CIB2	CPA1	CPA2	CTDSPL	EPB41	FLJ20152	FOXH1	FSHR	GAD2	HAS1	HES1	INSSA2	KCND1	KCTD7	LOC143286	MAFA	MAPK13	MEP1A	MUC1	NCR2	NRP2	PAK3	PMS2L5	PNLIPRP1	PRDM1	PTF1A	RANBP6	RBPJ	SEC15L2	SEL1L	SERPINI2	SPDEF	STX11	VASH1	YTHDC1	ZBTB25										

"Epithelium (21 genes included, 9 genes excluded)"																																																							
Included:	BCL10	CD46	CEACAM1	EGFR	ELF3	EPCAM	ERBB2	FGF10	GLI2	KRT14	KRT8	LAMA1	LAMB1	LAMC1	NME1	NME2	SPINK5	TGFA	TIMELESS	UPK1A	UPK1B																																		
Excluded:	CELSR1	DMBT1	EHF	KRT3	KRT4	LMO4	UPK2	UPK3A	VANGL2																																														

"Motor neuron (21 genes included, 4 genes excluded)"																																																							
Included:	FBXW7	HOXA1	HOXA5	HOXA9	HOXC4	HOXC9	ISL1	ISL2	MEF2C	MNX1	NCAM1	NEUROD1	NKX2-2	NKX6-1	NR2F1	OLIG2	ONECUT1	PAX6	PROX1	SHH	SOX1																																		
Excluded:	FOXO3	HOXA2	ONECUT2	POU2F1																																																			

"Monocytes-macrophages (25 genes included, 27 genes excluded)"																																																							
Included:	ANPEP	CD14	CD24	CD4	CD40	CD44	CD8A	CEACAM1	CEACAM5	CSF1R	FCGR3A	FCGR3B	FUT4	ICAM1	IFNGR1	ITGA4	ITGA6	ITGAL	ITGAM	ITGAX	ITGB1	ITGB2	PECAM1	PTPRC	THY1																														
Excluded:	CD1D	CD2	CD33	CD38	CD80	CD86	CD8B	CR1	CSF2RA	FCGR2A	FCGR2B	FCGR2C	IL1R1	IL1RN	IL2RA	IL6R	IL7R	LAMP1	LAMP2	MNDA	NMT1	SELE	SELL	SELP	SPN	TMEM176B	VNN2																												

"ISCI_geneSet (55 genes included, 38 genes excluded)"																																																							
Included:	AFP	CD34	CD9	CDH5	CDX2	COL1A1	COL2A1	CRABP2	DES	DNMT3B	EOMES	FN1	FOXA2	FOXD3	GATA4	GATA6	GCG	GFAP	INS	ISL1	KIT	KRT1	LAMA1	LAMB1	LAMC1	LEFTY1	LEFTY2	LIN28	MNX1	MYF5	MYOD1	NANOG	NES	NEUROD1	NODAL	NOG	OLIG2	PAX4	PAX6	PDX1	PECAM1	PODXL	POU5F1	RUNX2	SOX17	SOX2	SST	SYP	T	TDGF1	TERT	TH	UTF1	XIST	ZFP42
Excluded:	ACTC1	BXDC2	CGB	COMMD3	DDX4	DIAPH2	EDNRB	FGF4	FGF5	FLT1	GABRB3	GAL	GBX2	GCM1	GDF3	GRB7	HBB	HBZ	IAPP	IFITM1	IFITM2	IGF2BP2	IL6ST	LIFR	NPPA	NR5A2	NR6A1	NUMB	PTEN	PTF1A	REST	SEMA3A	SERPINA1	SFRP2	SYCP3	TAT	TFCP2L1	WT1																																																																																																		

"Computational_geneSet (61 genes included, 136 genes excluded)"																																																																																																																																								
Included:	ACE	BCL2	BDNF	BGN	BMP2	BMP4	BRCA1	CACNA1H	CD22	CD24	CD36	CD44	CDH1	CDH2	CDKN2A	CDKN2B	CDX2	CEACAM1	CHRNA7	CNTF	COL17A1	COL2A1	COL3A1	COMP	EPHB2	ERCC2	FGF7	FMO3	GATA2	GATA3	GATA4	HNF1B	HOXA9	IL8	INHBA	ITGA2B	ITGAX	ITGB3	JUN	KLF6	LAMA1	LPL	LRP2	MAPK14	MAPK3	MAPT	MME	MMP1	MPL	NCAM1	NGFR	PAX6	PML	PPARG	PPARGC1A	PXN	ROCK1	SRY	STAT3	THPO	TRAF2																																																																											
Excluded:	ABCA4	ABCC2	ACO1	ACPP	ADAMTS13	ALOX15	AMH	APBB1	AQP4	AR	AREG	AREGB	ARSA	ATP2A3	BIK	BMP7	CACNA1C	CALCRL	CASP10	CCKBR	CCL11	CCR5	CD82	CDC27	CDH13	CDH3	CFTR	CHRM3	CHRNE	CLCN1	CLDN1	CLDN3	CLDN4	COL10A1	COL4A6	CP	CX3CL1	CXCL12	CYP1A1	DARC	DCC	DDC	EIF4G1	ENPP1	ERBB3	F11	F13A1	F2RL1	F5	FBLN1	FBN1	FGF1	FLNA	FLT4	FOLH1	FOLR1	FOXC1	FRAP1	FSHR	GBA	GCK	GJB1	GNE	GSTA1	GSTT1	HIST1H2BC	HOXA10	HOXB7	HTR1B	IGFBP2	IGFBP5	IRS1	KCNA5	KCNQ1	L1CAM	LCAT	LMNA	LOX	LTC4S	MAGEA1	MAGEA2B	MAP4	MITF	MMP12	MMP3	MUC1	MUC4	NAMPT	NKX2-1	NOS3	NOX1	NPR1	NQO1	NR3C1	NR4A1	NRG1	NRP1	NUMA1	OPRM1	P2RX7	PAH	PAX8	PLA2G2A	POLG	PRDX2	PRKACA	PSMC2	PTGS2	PTN	RAD51	RAPGEF3	REN	RGS4	RPS6KA5	SCNN1B	SDC2	SERPINA5	SHBG	SLC16A1	SLC19A1	SLC26A4	SLC6A4	SMC1A	TACR1	TACSTD1	TLR4	TNFRSF11B	TOP2A	TOR1A	TRPV6	TSHR	UCP2	UGT1A1	VCL	VDAC1	VIP

"DNA_methylation_mostVariable (21 genes included, 29 genes excluded)"																																																																																																																																								
Included:	CALCB	CAT	CD14	COMT	CRCT1	CYP2E1	FAM24B	HIST1H3C	HTRA4	MOS	NPY	PAPOLB	PEG3	PF4	PON3	POU5F1	RLN1	RLN2	S100A6	TF	ZNF737																																																																																																																			
Excluded:	AGBL2	AKAP12	ASB3	C12orf56	CCDC11	CR1L	CRYGD	CSRP1	DENND2D	GP5	KAAG1	KBTBD12	PAQR6	PCDHA2	PKD2L2	PLEK2	PPYR1	PRDXDD1P	RAET1L	REM1	RGPD2	SLFN13	ST8SIA4	ZNF248	ZNF354C	ZNF454	ZNF528	ZNF667	ZNF876P																																																																																																											

"Gene_expression_mostVariable (20 genes included, 30 genes excluded)"																																																																																																																																								
Included:	AFP	APOA1	APOA2	CAT	COL3A1	CXCR4	DLK1	FGB	FGG	FOS	GREM1	HOXA1	LEFTY1	LEFTY2	MEG3	MMP1	MSX1	NR2F1	PAX6	TTR																																																																																																																				
Excluded:	APOB	CER1	CH25H	COL6A3	CST1	DKK1	EGR1	EGR3	FZD10	HAPLN1	HOXB2	IGFBP7	LGI1	LRRC17	LRRN3	LUM	MEIS2	NLRP2	NPPB	NPTX1	PTX3	PYCR2	SERPINA1	STMN2	TFF1	TGFBI	TRBC1	TRBC2	WLS	ZIC1																																																																																																										
