TABLE 14: Alternative Gene Set for DNA methylation gene set or Gene Expression  or lineage marker propensity differentiation assay (small Subgroup)																												
All categories (363 genes)			Ectoderm germ layer (51 genes)	Mesoderm germ layer (87 genes)	Endoderm germ layer (36 genes)	Pluripotent cell signature (59 genes)	Male/female classification (5 genes)	Neural lineage (92 genes)	Hematopoietic lineage (89 genes)	Epidermis (38 genes)	Mesenchymal stem cell (70 genes)	Bone (21 genes)	Cartilage (21 genes)	Fat (21 genes)	Muscle (40 genes)	Blood vessel (62 genes)	Heart (39 genes included)	Lymphoid cells (42 genes)	Myeloid cells (42 genes)	Liver (21 genes)	Pancreas (22 genes)	Epithelium (21 genes)	Motor neuron (21 genes)	Monocytes-macrophages (25 genes)	ISCI_geneSet (55 genes)	Computational_geneSet (61 genes)	DNA_methylation_mostVariable (21 genes)	Gene_expression_mostVariable (20 genes)
ABCB1	DNMT3B	ISL1	ABCB1	ABCB1	ALB	ABCG2	DDX3X	ABCB1	ABCB1	BCL2	ACAN	ALPL	ACAN	ADIPOQ	ACTA1	ACE	ACTA1	ANPEP	ANPEP	AFP	ERCC2	BCL10	FBXW7	ANPEP	AFP	ACE	CALCB	AFP
ABCG2	E2F1	ISL2	ABCG2	ABCG2	APOE	ALPL	DDX3Y	ABCG2	ABCG2	CHUK	ACTA2	ALX1	ALX1	BMPR1A	ACTA2	ACTA2	ACTA2	BMPR1A	CARTPT	ALB	FOXA2	CD46	HOXA1	CD14	CD34	BCL2	CAT	APOA1
ACAN	EBF1	ITGA2B	APOE	ACTA2	CD44	CAMK2A	RPS4Y1	APOE	ACE	COL17A1	ADIPOQ	BGLAP	BMP2	CD34	ACTB	BMPER	ACTN1	CD14	CD14	APOE	GCG	CEACAM1	HOXA5	CD24	CD9	BDNF	CD14	APOA2
ACE	EGF	ITGA4	CD24	ACTB	CDCP1	CD24	SRY	BMP2	ALB	COL1A1	ALPL	BGN	BMPER	CEBPB	ACTN1	CD14	BMP2	CD19	CD24	CD44	HHEX	EGFR	HOXA9	CD4	CDH5	BGN	COMT	CAT
ACTA1	EGFR	ITGA6	CD44	ACTN1	CDH2	CD9	XIST	BMP4	ANPEP	CRABP2	ALX1	BMP2	CD151	CEBPG	BMP4	CD151	CAMK2A	CD22	CD34	CEBPB	INS	ELF3	HOXC4	CD40	CDX2	BMP2	CRCT1	COL3A1
ACTA2	ELF3	ITGAL	CDH2	ADIPOQ	CDX2	CDH1		CAMK2A	BMI1	EGF	ANPEP	BMP4	CD44	DLK1	CACNA1H	CD34	CD34	CD24	CD36	FABP1	ISL1	EPCAM	HOXC9	CD44	COL1A1	BMP4	CYP2E1	CXCR4
ACTB	EN1	ITGAM	CRABP2	ANPEP	CTNNB1	CDKN2A		CD24	BMPR1A	EGFR	BGLAP	CARTPT	COL2A1	EN1	CAPN1	CD36	CDH15	CD28	CD4	FMO3	ITGA6	ERBB2	ISL1	CD8A	COL2A1	BRCA1	FAM24B	DLK1
ACTN1	ENG	ITGAV	CXCR4	BMP2	CXCR4	CDX2		CD34	CD14	ERCC2	BGN	COL1A1	COL3A1	FABP2	CDH15	CDH2	CDH2	CD34	CD40	FOXA2	MNX1	FGF10	ISL2	CEACAM1	CRABP2	CACNA1H	HIST1H3C	FGB
ADIPOQ	ENO3	ITGAX	EN1	CAPN1	DLX5	CREBBP		CDH2	CD19	EREG	BMP2	COL3A1	COL4A2	FABP3	CDH2	CDH5	CDH5	CD3E	CD44	GATA4	NEUROD1	GLI2	MEF2C	CEACAM5	DES	CD22	HTRA4	FGG
AFP	EOMES	ITGB1	FAS	CD14	FABP1	CTNNB1		CEACAM1	CD22	FGF7	BMPER	DCN	COL4A4	FABP4	COL4A4	CHRNA7	CEACAM1	CD4	CD8A	HHEX	NEUROG3	KRT14	MNX1	CSF1R	DNMT3B	CD24	MOS	FOS
ALB	EP300	ITGB2	FGFR2	CD151	FABP2	DDX3X		CEACAM5	CD24	FOS	BMPR1A	DMP1	COMP	HOXA1	DES	COL4A2	DES	CD40	CEACAM1	HNF1A	NKX2-2	KRT8	NCAM1	FCGR3A	EOMES	CD36	NPY	GREM1
ALPL	EPCAM	ITGB3	FN1	CD19	FOXA1	DLL1		CNTF	CD28	HRAS	CD14	FN1	CRTAC1	HOXA5	DMD	CSF1R	ERBB2	CD44	CEACAM5	HNF1B	NKX6-1	LAMA1	NEUROD1	FCGR3B	FN1	CD44	PAPOLB	HOXA1
ALX1	EPHB2	JAG1	FUT4	CD24	FOXA2	E2F1		CXCR4	CD34	ITGA6	CD34	GDF10	DMP1	HOXC4	ENO3	CXCR4	FABP3	CD8A	CEBPG	HNF4A	ONECUT1	LAMB1	NKX2-2	FUT4	FOXA2	CDH1	PEG3	LEFTY1
ANPEP	EPHB4	JMJD6	GATA2	CD34	GATA3	EP300		DLK1	CD36	JUN	CD3E	GLI2	EPYC	HOXC9	EREG	EGF	FCGR3A	CEACAM1	CSF1R	HTATSF1	PAX4	LAMC1	NKX6-1	ICAM1	FOXD3	CDH2	PF4	LEFTY2
APOA1	EPO	JUN	GATA3	CD36	GATA4	EPCAM		DLL1	CD3E	KRT1	CD44	IGFBP3	FMOD	LPL	FABP3	ENG	FCGR3B	CEACAM5	ENG	ITGA6	PAX6	NME1	NR2F1	IFNGR1	GATA4	CDKN2A	PON3	MEG3
APOA2	EPYC	KDR	GFAP	CD4	GATA6	EPHB2		DLX5	CD4	KRT14	CEACAM1	MSX1	GAS6	LRP2	FGF8	EPHB4	GATA2	CEBPG	ETV2	ITGB1	PDX1	NME2	OLIG2	ITGA4	GATA6	CDKN2B	POU5F1	MMP1
APOE	ERAS	KIT	HAND1	CD44	GCG	ERAS		EN1	CD40	KRT5	CEACAM5	RUNX2	GDF10	NR2F1	GATA4	EPO	GATA4	FAS	FCGR3A	ONECUT1	PML	SPINK5	ONECUT1	ITGA6	GCG	CDX2	RLN1	MSX1
BCL10	ERBB2	KLF4	ICAM1	CD59	HNF1A	FGF10		EOMES	CD44	MAP2K1	COL1A1	SOX9	SCXA	PECAM1	GATA6	FCGR3A	GLI2	FASLG	FCGR3B	PROX1	RUNX2	TGFA	PAX6	ITGAL	GFAP	CEACAM1	RLN2	NR2F1
BCL2	ERCC2	KLF6	ITGA4	CD9	HNF1B	FGF2		EPHB4	CD59	MAP3K1	COL2A1	SP7	SIX2	PPARG	GLMN	FCGR3B	HAND1	FCGR3A	FUT4	RXRA	SLC2A2	TIMELESS	PROX1	ITGAM	INS	CHRNA7	S100A6	PAX6
BDNF	EREG	KRT1	ITGA6	CDCP1	HTATSF1	FOXD3		FAS	CD8A	MAPK1	COL3A1	SPARC	SOX9	PPARGC1A	IGFBP3	FGF10	ISL1	FCGR3B	GAS6	TBX3	SOX9	UPK1A	SHH	ITGAX	ISL1	CNTF	TF	TTR
BGLAP	ERG	KRT14	ITGB1	CDH1	ISL1	FUT4		FCGR3A	CD9	MAPK14	COL4A2	THPO	VNN1	THBD	MCAM	FGF2	KDR	GATA3	HLA-DRA	THY1	SST	UPK1B	SOX1	ITGB1	KIT	COL17A1	ZNF737	
BGN	ETV2	KRT5	JAG1	CDH15	ITGA6	GNL3		FCGR3B	CDCP1	MAPK3	COL4A4				MEF2C	FGF8	KIT	HLA-DRA	IFNGR1		SYP			ITGB2	KRT1	COL2A1		
BMI1	FABP1	KRT8	MAP2	CDH2	ITGB1	GREM1		FGF2	CDH1	MAPK8	COMP				MKL1	FGFR2	MEF2C	ICAM1	IL4					PECAM1	LAMA1	COL3A1		
BMP2	FABP2	LAMA1	MAPT	CDH5	LRP2	GSK3B		FGF8	CDH2	NFKB1	CRTAC1				MYF5	FGFR3	MKL1	IFNGR1	INHBA					PTPRC	LAMB1	COMP		
BMP4	FABP3	LAMB1	MCAM	CEACAM1	NEUROG3	IFNGR1		FGFR2	CDH5	NFKBIA	CSF1R				MYH3	FUT4	MYH3	IL12B	ITGA2B					THY1	LAMC1	EPHB2		
BMPER	FABP4	LAMC1	MNX1	CSF1R	NKX2-5	IRF6		FGFR3	CEACAM1	NME2	DCN				MYL2	GLMN	MYL2	IL4	ITGA6						LEFTY1	ERCC2		
BMPR1A	FAM24B	LEF1	NCAM1	CXCR4	PAX6	ITGA6		FN1	CEACAM5	PRKCA	DES				MYOD1	HOXA9	MYOG	INHBA	ITGAL						LEFTY2	FGF7		
BRCA1	FAS	LEFTY1	NEFL	DES	PDX1	ITGB1		FOXD3	CSF1R	PRKCB1	DMD				MYOG	ICAM1	NKX2-5	ITGAL	ITGAM						LIN28	FMO3		
CACNA1H	FASLG	LEFTY2	NES	DLL1	SLC2A2	JAG1		FUT4	CXCR4	RAF1	DMP1				NKX2-5	IL8	NOTCH1	ITGAM	ITGAV						MNX1	GATA2		
CALCB	FBXW7	LIN28	NEUROG3	ENG	SOX17	JMJD6		GDNF	DLK1	RELA	ENG				NOTCH1	INHBA	PECAM1	ITGAV	ITGAX						MYF5	GATA3		
CAMK2A	FCGR3A	LMX1A	NGFR	ENO3	SOX7	KIT		GFAP	DLL1	SP1	FABP3				PAX3	ITGA2B	SHH	ITGAX	ITGB2						MYOD1	GATA4		
CAPN1	FCGR3B	LPL	NOG	FABP4	SPARC	KLF4		GLI2	EBF1	SPINK5	FABP4				PAX7	ITGA4	SRF	ITGB2	ITGB3						NANOG	HNF1B		
CARTPT	FGB	LRP2	NOTCH1	FCGR3A	SST	LIN28		GNL3	ENG	TFRC	FCGR3A				SOX10	ITGA6	T	KIT	KIT						NES	HOXA9		
CAT	FGF10	MAP2	OTX2	FCGR3B	SYP	MAP2K1		HMGA2	EPHB4	TGFB2	FCGR3B				TAZ	ITGAV	TAZ	MME	MPL						NEUROD1	IL8		
CD14	FGF2	MAP2K1	PAX3	FN1	THY1	MAPK1		ICAM1	EPO	TNF	FGF8				TBX3	ITGB1	TDGF1	NCAM1	PECAM1						NODAL	INHBA		
CD151	FGF7	MAP3K1	PAX5	FOXA2	VIM	MAPK3		ISL1	ERG	TNFRSF1A	FMOD				TGFB1	ITGB2	TGFB2	PECAM1	PF4						NOG	ITGA2B		
CD19	FGF8	MAPK1	PAX6	FUT4		MYC		ISL2	ETV2	TNFRSF1B	FN1				TNNI3	ITGB3	TNNI3	PTPRC	PTPRC						OLIG2	ITGAX		
CD22	FGFR2	MAPK14	PAX7	GATA3		NANOG		ITGA4	FAS	TRAF2	FUT4				TNNT2	JAG1	TNNT2	SDC1	RUNX1						PAX4	ITGB3		
CD24	FGFR3	MAPK3	PDGFRA	GATA4		NEUROG3		ITGA6	FASLG		GAS6				TWIST1	KDR	VCAM1	SPEN	SPI1						PAX6	JUN		
CD28	FGG	MAPK8	S100B	GSC		NODAL		ITGAM	FCGR3A		GATA4				VIM	KIT		SPINK5	TFRC						PDX1	KLF6		
CD34	FMO3	MAPT	SNAI2	HAND1		NOTCH1		ITGB1	FCGR3B		GDF10					MCAM		TFRC	THY1						PECAM1	LAMA1		
CD36	FMOD	MCAM	SOX10	HHEX		PODXL		JAG1	FUT4		GLMN					MKL1		THY1	ZBTB16						PODXL	LPL		
CD3E	FN1	MEF2C	SOX2	HLA-DRA		POU5F1		LAMB1	GAS6		GNL3					NCAM1									POU5F1	LRP2		
CD4	FOS	MEG3	SOX9	ICAM1		PROM1		LIN28	GATA1		ITGAM					NES									RUNX2	MAPK14		
CD40	FOXA1	MKL1	SYP	IGFBP3		RAF1		LMX1A	GATA2		ITGB1					PECAM1									SOX17	MAPK3		
CD44	FOXA2	MME	SYT1	INHBA		ROCK1		MAP2	GATA3		KIT					PF4									SOX2	MAPT		
CD46	FOXD3	MMP1	TDGF1	ITGA2B		SHH		MAPT	HLA-DRA		LPL					PML									SST	MME		
CD59	FUT4	MNX1	TH	ITGA4		SOX17		MCAM	HOXB4		MEF2C					PODXL									SYP	MMP1		
CD8A	GAS6	MOS	THY1	ITGA6		SOX2		MEF2C	ICAM1		MKL1					PTPRC									T	MPL		
CD9	GATA1	MPL	TP63	ITGAL		SP1		MNX1	IFNGR1		MME					RUNX1									TDGF1	NCAM1		
CDCP1	GATA2	MSI1	VIM	ITGAM		STAT1		MSI1	IL4		MYF5					SHH									TERT	NGFR		
CDH1	GATA3	MSX1		ITGAV		STAT3		MSX1	IRF6		MYL2					SPARC									TH	PAX6		
CDH15	GATA4	MYC		ITGAX		STAT5A		NCAM1	ITGA2B		MYOG					SPINK5									UTF1	PML		
CDH2	GATA6	MYF5		ITGB1		TDGF1		NEFL	ITGA4		NGFR					STAT3									XIST	PPARG		
CDH5	GCG	MYH3		ITGB2		TERT		NES	ITGA6		NKX2-5					TGFB2									ZFP42	PPARGC1A		
CDKN2A	GDF10	MYL2		ITGB3		TGIF1		NEUROD1	ITGAL		PAX3					THBD										PXN		
CDKN2B	GDNF	MYOD1		KDR		UTF1		NEUROG1	ITGAM		PAX7					THY1										ROCK1		
CDX2	GFAP	MYOG		KIT		ZFP42		NGFR	ITGAV		PECAM1					TNFRSF1A										SRY		
CEACAM1	GLI2	NANOG		LEF1		ZFX		NKX2-5	ITGAX		PPARG					TNFRSF1B										STAT3		
CEACAM5	GLMN	NCAM1		MCAM				NOG	ITGB2		RUNX2					TNNI3										THPO		
CEBPB	GNL3	NEFL		MME				NOTCH1	ITGB3		SCXA					VCAM1										TRAF2		
CEBPG	GREM1	NES		MYH3				NR2E1	JAG1		SIX2					VIM												
CHRNA7	GSC	NEUROD1		MYOD1				OLIG2	JMJD6		SOX9																	
CHUK	GSK3B	NEUROG1		MYOG				OTX2	KDR		SP7																	
CNTF	HAND1	NEUROG3		NCAM1				PAX3	KIT		SPARC																	
COL17A1	HHEX	NFKB1		NES				PAX5	KLF6		THPO																	
COL1A1	HIST1H3C	NFKBIA		NGFR				PAX6	MME		TNFRSF1A																	
COL2A1	HLA-DRA	NGFR		NODAL				POU5F1	MPL		TNNT2																	
COL3A1	HMGA2	NKX2-2		NOTCH1				PROM1	NCAM1		VCAM1																	
COL4A2	HNF1A	NKX2-5		PECAM1				PTPRC	NOTCH1		VNN1																	
COL4A4	HNF1B	NKX6-1		PTPRC				RUNX1	PECAM1																			
COMP	HNF4A	NME1		SDC1				S100B	PODXL																			
COMT	HOXA1	NME2		SPI1				SDC1	PROM1																			
CRABP2	HOXA5	NODAL		SRF				SHH	PTPRC																			
CRCT1	HOXA9	NOG		STAT3				SNAI2	RUNX1																			
CREBBP	HOXB4			T				SOX1	SDC1																			
CRTAC1	HOXC4			TAZ				SOX10	SPEN																			
CSF1R	HOXC9			TFRC				SOX2	T																			
CTNNB1	HRAS			TGFB1				SOX4	TAL1																			
CXCR4	HTATSF1			THBD				SOX9	TFRC																			
CYP2E1	HTRA4			THY1				SYP	THBD																			
DCN	ICAM1			TNFRSF1A				SYT1	THPO																			
DDX3X	IFNGR1			TNFRSF1B				TCF3	THY1																			
DDX3Y	IGFBP3			TNNI3				TCF4	TNF																			
DES	IL12B			TWIST1				TFRC	TNFRSF1A																			
DLK1	IL4			VCAM1				TGFB2	VCAM1																			
DLL1	IL8			VIM				TGIF1	VNN1																			
DLX5	INHBA							TH	ZBTB16																			
DMD	INS							THY1	ZFX																			
DMP1	IRF6							TUBB3																				
								TWIST1																				
								VIM																				
