18-gene_MEK pathway_activation_signature	adopted from ref 6	KANK1	DUSP4	DUSP6	ELF1	ETV4	ETV5	FXYD5	LGALS3	LZTS1	MAP2K3	PHLDA1	PROS1	S100A6	SERPINB1	SLCO4A1	SPRY2	TRIB2	ZFP106
13-gene_MEKi_bypass_resistance_signature	adopted from ref 6	BASP1	CD274	CLU	COL12A1	COL5A1	CRIM1	FZD2	G0S2	GPR176	IL6	LOX	SERPINE1	STAC
SRC_activation	adopted from ref 27	ABLIM3	ADD1	ADH1B	AKR1C1	AKR1C2	ALPP	ANKHD1	APP	ATOH8	ATP1A1	ATP2C1	ATP6V1D	BEST2	C5orf42	CADM3	CCDC80	CFB	CLASP2	COL12A1	COL28A1	COL8A1	CXCR4	CYP4B1	DCN	DKK1	EIF4A2	FBN1	FBXO32	FLVCR2	FN1	FPR1	GALNTL2	GRB10	HAS2	HSPA8	KANK2	MAP1B	MAP2	MME	MMP2	MYBPC1	NAPRT1	NEDD9	NUMA1	PAPPA	PAPPA-AS1	PARP9	PHF17	PLEC	PSAP	RPS24	RTN1	SERPINE2	SETD2	SETD5	SMARCA2	SRGN	STAU1	TFPI	WNT5A	ZCCHC6
5-gene dasatinib sensitivity signature	adopted from ref 28	EPHA2	CAV1	CAV2	ANXA1  PTRF
Hu-Lgr5-ISC	adopted from ref 29 	ABTB2	AFAP1L1	APCDD1	ARHGEF4	ARNT2	AXIN2	BCL2	BEX1	BEX2	CAP2	CCDC46	CYP2E1	DGKG	DLGAP1	DTL	DYNC2H1	EPHA4	FAM64A	FGFR4	FMNL2	FSTL1	GRAMD1A	GRK4	IGF1R	IGFBP4	IL17RD	KIF12	KIF26B	KLHL13	LDHB	LGR5	LIFR	LOC285141	MDFIC	MPP3	NPNT	PITPNC1	PLP1	RASSF4	RNF157	SCN2B	SEPT6	SERTAD4	SLC1A2	SLC38A4	SLCO3A1	SLIT2	SOAT1	SORBS2	SOX4	TACC1	TMEM182	TNFRSF19	UTRN	ZNF141	ZNF273	ZNF493	ZNF626	ZNF678	ZNF680	ZNF714	ZNF85	ZNF92	ZNF93
Hu-EphB2-ISC	adopted from ref 29	ASRGL1	BCL2	BEX1	BEX2	CD44	CENPF	CYP2E1	EPHB3	FMNL	FSTL1	IGFBP4	KIF26B	LGR5	MPP3	PRELP	PSRC1	PTHLH	PTPRO	PVT1	SCN2B	SLC1A2	SLC38A4	SLCO3A1	SOAT1	SORBS2	ST3GAL3	TACC1	TEAD2	TNFRSF19
Hu-Late_TA	adopted from ref 29	ACE2	AKR1B10	ALPI	ANPEP	CD36	CLIC5	CYP2C8	EGLN3	EMP1	ENPP3	F3	FMO5	FRMD3	GDA	GDPD2	HKDC1	IGSF9	IL18	KRT20	LRRC19	MAFB	MALL	MGAT4C	MME	OAS3	OSGIN1	OSTalpha	PAPSS2	PCK1	PFKP	PLEKHG6	PTK6	RAB30	RHOC	SLC13A1	SLC15A1	SLC23A1	SLC26A3	SLC26A6	SLC2A2	SLC2A5	SLC30A10	SLC5A12	SLC6A19	SLC9A3	SLITRK6	ST3GAL4	SYNPO	TREH	TRIM15	VWA1
Hu-Proliferation	adopted from ref 29	ANLN	AQP4	ASF1B	ATAD2	ATIC	ATR	AURKA	AURKB	BAG2	BARD1	BBS7	BCL7A	BLM	BRCA1	BUB1	BUB1B	C12orf48	C14orf106	C15orf23	C17orf53	C1orf112	C3orf26	C8orf79	CCDC14	CCDC99	CCNA2	CCNE1	CCNF	CD55	CDC45L	CDC6	CDC7	CDCA2	CDCA5	CELSR2	CENPE	CENPF	CENPI	CENPN	CEP192	CEP55	CHAF1B	CHEK1	CHTF18	CKAP2L	CLSPN	CRTAC1	CTPS	CYP39A1	DACH1	DCK	DCTD	DEPDC1	DIAPH3	DKC1	DNAH11	DNAJC18	DOCK4	DTL	DUS4L	ESCO2	EXO1	EXOSC2	EXOSC8	FBXL7	FEN1	FIGNL1	FOXM1	GEMIN4	GEMIN5	GINS1	GINS2	GINS3	GSTCD	HELLS	HEMGN	HMGA2	HMMR	IGF1R	ILF3	INTU	IQGAP3	KBTBD6	KCNN4	KIF11	KIF22	KIF4A	KIFC1	LAMC1	LIG1	LPHN1	LYAR	MBD4	MCM2	MCM3	MCM4	MCM5	MCM7	MCM8	MDN1	MELK	MITF	MLF1IP	MPHOSPH9	MTHFD2	MYB	MYBL2	MYC	MYO5A	NAP1L1	NCAPD2	NCAPG2	NCAPH	NDE1	NEK2	NETO2	NEXN	NUF2	NUP133	NUP85	NUSAP1	PAICS	PALB2	PBK	PBX3	PFAS	PGM2L1	PLAGL1	PLK1	POLA1	POLD1	POLE2	POLI	POLR1E	PRKD3	PRR11	PSIP1	PUS7	QTRT1	RAD18	RAD51	RAD51AP1	RAD51C	RAD54B	RAD54L	RASA3	RCC2	RFC3	RPA2	RPP40	RPUSD2	RRM1	RRM2	SACS	SCML2	SGOL1	SGOL2	SIVA1	SLC12A2	SLC39A8	SLFN13	SMC2	SPAG5	TACC3	TBC1D19	TBC1D4	TCF19	TIMELESS	TIMP3	TK1	TMEM107	TOPBP1	TPX2	TRAIP	TSGA14	TSPAN12	TUBB	TUBE1	UBE2T	UHRF1	UNG	UTP15	VRK1	WDHD1	WDR35	XRCC2	ZC3H7B	ZNF275	ZNF367	ZNF473	ZNF704	ZNRF3
EMT_UP	adopted from ref 22,25	ADAM23	ADAMTS1	AFF3	AK5	AKAP12	ALPK2	ANGPTL2	ANKRD1	ANTXR1	ANXA6	AOX1	AP1S2	ARMCX1	ATP8B2	ATP8B3	AXL	BDNF	BICC1	BNC2	BVES	C10orf38	C10orf56	C16orf45	C1S	C9orf19	CAP2	CCL2	CDH11	CDH2	CDH4	CHN1	CLDN11	CLIP3	CMTM3	COL12A1	COL1A2	COL3A1	COL4A1	COL5A1	COL5A2	COL6A1	CPA4	CTGF	CYBRD1	DAB2	DFNA5	DIO2	DKK3	DLC1	DOCK10	DPYSL3	EDIL3	ELOVL2	EML1	EMP3	EPB41L5	EPDR1	EVI2A	F2R	FAM101B	FAT4	FBN1	FGF2	FGF5	FGFR1	FHL1	FLRT2	FSTL1	GFPT2	GLIPR1	GLT25D2	GNB4	GNG11	GPC6	GPR176	GREM1	HAS2	HEG1	HS3ST3A1	HTRA1	IGFBP7	IL13RA2	JAM3	KIRREL	LAMA4	LEPREL1	LGALS1	LHFP	LIX1L	LOX	MAP1B	MMP2	MRAS	MSRB3	NAP1L3	NAV3	NDN	NEGR1	NEXN	NID1	NRG1	NUDT11	PAPPA	PDE7B	PLAGL1	PMP22	PNMA2	POPDC3	POSTN	PRKD1	PRR16	PTGIS	PTRF	PTX3	RBM24	RBMS3	RBPMS2	RECK	RFTN1	SERPINE1	SIRPA	SLC2A3	SLC47A1	SPARC	SRGN	SRPX	ST3GAL2	SUSD5	SYDE1	TBXA2R	TCF4	TGFB2	TMEM158	TMEM47	TMSL8	TNFRSF19	TRPA1	TTC28	TTLL7	TUB	TUBA1A	UCHL1	VIM	WIPF1	WNT5B	ZEB1	ZEB2	ZFPM2	ZNF788
EMT_DOWN	adopted from ref 22,25	ACPP	AGR3	ALDH3B2	ANK3	ANKRD22	ANXA9	AP1M2	AQP3	ARHGAP8	ARHGDIB	ATAD4	ATP2C2	B3GNT3	BLNK	BSPRY	C11orf52	C19orf21	C1orf106	C1orf116	C1orf210	C1orf34	CCDC64B	CD24	CDH1	CDH3	CDS1	CEACAM5	CEACAM6	CGN	CKMT1B	CLDN4	CLDN7	CNKSR1	CNTNAP2	CTAGE4	DAPP1	DENND2D	DMKN	DSC2	DSP	EHF	ELF3	ELF5	EPN3	EPPK1	ERBB3	ERP27	FA2H	FAAH2	FAM110C	FAM83A	FAM84A	FAM84B	FBP1	FGD2	FGFBP1	FUT1	FUT3	FXYD3	GALNT3	GCNT3	GJB6	GOLT1A	GPR110	GPR87	GPX2	GRAMD2	GRHL1	GRHL2	HOOK1	HS3ST1	HS6ST2	IL1RN	ILDR1	INPP4B	IRF6	ITGB6	KLK10	KLK5	KLK6	KLK8	KRT16	KRT19	KRT5	KRTCAP3	LAMA3	LAMB3	LAMC2	LCN2	LCP1	LIPG	MAL2	MAP7	MAPK13	MARVELD2	MARVELD3	MB	MBNL3	MPP7	MUC20	MYH14	MYO5B	NPNT	OR2A4	OVOL2	PAK6	PKP3	PLA2G10	POU2F3	PPL	PPP1R14C	PROM2	PRR15	PRSS8	PTAFR	PVRL4	RAB25	RAPGEF5	RASEF	RASGEF1B	RBM35A	RBM35B	S100A14	S100A8	S100A9	S100P	SCEL	SCNN1A	SERPINB5	SH2D3A	SH3YL1	SLC6A14	SLPI	SORBS2	SPINK5	SPINT1	SPINT2	SPRR1A	SPRR1B	SPRR3	ST14	STEAP4	STX19	SYK	SYT7	TMC4	TMC5	TMEM125	TMEM30B	TMEM45B	TMPRSS11E	TMPRSS13	TMPRSS4	TOX3	TRIM29	TSPAN1	TTC22	TTC9	VTCN1	WDR72	WFDC2
PC1_UP	adopted from ref 22,25	AEBP1	AKAP12	AKT3	AMOTL1	ANKRD6	AP1S2	ARMCX1	ARMCX2	ATP8B2	BASP1	BGN	C1orf54	C20orf194	CALD1	CAP2	CCDC80	CEP170	CFH	CFL2	CMTM3	COX7A1	CRYAB	DCN	DFNA5	DNAJB4	DPYSL3	DZIP1	ECM2	EFHA2	EFS	EHD3	FAM20C	FBXL7	FEZ1	FLRT2	FRMD6	GFPT2	GLIS2	GNG11	HECTD2	HTRA1	IL1R1	JAM3	KCNE4	KIAA1462	KLHL5	LAYN	LDB2	LGALS1	LHFP	LIX1L	LMCD1	LPHN2	LZTS1	MAF	MAGEH1	MAP1B	MAP9	MCC	MGP	MLLT11	MPDZ	MRAS	MSN	MSRB3	MXRA7	MYH10	MYO5A	NAP1L3	NDN	NNMT	NR3C1	NRP1	NRP2	PEA15	PFTK1	PHLDB2	PKD2	PRICKLE1	PRKD1	PTPRM	PTRF	QKI	RAB31	RAB34	RAI14	RASSF8	RECK	RGS4	RNF180	SCHIP1	SDC2	SERPINF1	SGCE	SGTB	SLIT2	SMARCA1	SNAI2	SPARC	SPG20	SRGAP2	SRPX	STON1	SYT11	TCEA2	TCEAL3	TIMP2	TNS1	TPST1	TRPA1	TRPC1	TRPS1	TSPYL5	TTC7B	TUBB6	TUSC3	UBE2E2	UCHL1	VIM	WWTR1	ZFPM2	ZNF25	ZNF532	ZNF677
PC1_DOWN	adopted from ref 22,25	ACOT11	AGMAT	ANKS4B	AP1M2	ATP10B	AXIN2	BCAR3	BCL2L14	BDH1	BRI3BP	C10orf99	C4orf19	C9orf152	C9orf75	C9orf82	CALML4	CAPN5	CASP5	CASP6	CBLC	CC2D1A	CCL28	CDC42EP5	CDS1	CDX1	CKMT1B	CLDN3	CMTM4	CORO2A	COX10	CYP2J2	DAZAP2	DDAH1	DTX2	DUOX2	DUOXA2	ENTPD5	EPB41L4B	EPHB2	EPN3	EPS8L3	ESRRA	ETHE1	EXPH5	F2RL1	FA2H	FAM3D	FAM83F	FAM84A	FRAT2	FUT2	FUT3	FUT4	FUT6	GALNT7	GMDS	GPA33	GPR35	GPX2	HDHD3	HMGA1	HNF4A	HOXB9	HSD11B2	KALRN	KCNE3	KCNQ1	KIAA0152	LENG9	LGALS4	LRRC31	MAP7	MARVELD3	MCCC2	MPST	MRPS35	MUC3B	MYB	MYH14	MYO5B	MYO7B	NAT2NOB1	NOX1	NR1I2	PAQR8	PI4K2B	PKP2	PLA2G12A	PLEKHA6	PLS1	PMM2	POF1B	PPP1R1B	PREP	RAB25	RNF186	SELENBP1	SH3RF2	SHH	SLC12A2	SLC27A2	SLC29A2	SLC35A3	SLC37A1	SLC44A4	SLC5A1	SLC9A2	ST14	STRBP	SUCLG2	SULT1B1	TJP3	TMC5	TMEM54	TMPRSS2	TST	USP54	XK
64-gene_WNT	aadopted from ref 3,26	ABCB1	ADAM10	ALEX1	ASCL2	AXIN2	BAMBI	BCL2L2	BIRC5	BMI1	BMP4	CCND1	CD44	CDKN2A	CDX1	CLDN1	PTGS2	DKK1	DKK4	DNMT1	EDN1	ENC1	EPHB2	EPHB3	FGF18	FGFBP	FRA1	FSCN1	GAST	NEDD9	HES1	ID2	TCF4	JAG1	JUN	L1CAM	LAMC2	LEF1	LGR5	MENA	MET	MMP14	MMP7	MYB	MYC	MYCBP	NOS2	NOTCH2	NRCAM	PLAU	PLAUR	PPARD	S100A4	S100A6	SGK1	SMC3	SOX9	SP5	SFRS3	SUZ12	TCF1	TIAM1	TN-C	VEGF	YAP1