. 2015 Apr 14;6(2):e00441-15. doi: 10.1128/mBio.00441-15

TABLE 2 .

Predicted upstream regulators of genes with 1.5-fold expression change in CTAR1-expressing cells

Upstream regulator	Predicted activation state	z score	P value of overlap	Target molecules in data set
MAP3K7 (TAK1)^a	Inhibited	−2.14	3.09E−05	BIRC3, CH25H, IFIH1, ITGB1, MMP3, PTGS2, RGS2, TNFSF10, VHL
TNF^b	Activated	2.04	1.89E−24	ADM, ALCAM, AMH, ANGPT1, ANPEP, ANXA1, APLN, APOBEC3B, ATP2A2, BIRC2, BIRC3, BTG2, CAT, CAV1, CCND2, CD36, CDKN2A, CDKN2C, CEBPA, CEBPB, CH25H, COL3A1, COTL1, CSF1, CTNNB1, CYBA, CYLD, CYR61, DAG1, DDX58, DKK1, DMD, EGFR, EGR1, EMP2, ENPP2, FERMT1, FGFR1, GNAI1, GPR176, HPGD, ID1, IFIH1, IGFBP2, IGFBP4, IL1R1, IL4R, ITGAV, ITGB1, JAG1, JUNB, KITLG, KLF5, KLF6, LGALS3, LRP6, MET, MIF, MMP10, MMP14, MMP3, NEFH, NFKB1, NFKB2, NFKBIZ, NID1, NME1, NRIP1, PDGFRA, PDPN, PDX1, PHLDA1, PLK2, PMAIP1, PROK2, PSMB9, PTEN, PTGS2, RASD1, RBP1, RELB, RGS2, RGS5, ROBO1, SDC4, SERPINE2, SGK1, SHH, SIRT1, SNAI1, SOCS1, SOD2, SP3, STAT1, TAPBP, TEK, TFPI, TFPI2, TIMP3, TJP1, TNFRSF6B, TNFSF10, TRAF2, TRAF3, TRAF6, VEGFA, VEGFC, VIM, WLS, WTAP, YY1
CHUK (IKKα)^b	Activated	2.08	8.20E−07	CEBPB, CH25H, COL18A1, CSF1, CYBA, ENPP2, JUNB, KLF5, MFAP5, MMP3, NFKB2, NID1, PTGS2, RBP1, RELB, SERPINE2, SGK1, VEGFA, VEGFC
TRAF2^a	Activated	2.36	2.70E−06	ADM, BIRC2, BIRC3, CDKN2A, CYLD, EGFR, ITGB1, LRRC16A, NFKB1, PLBD1, TRAF2
GSK3B^a	Activated	2.45	8.34E−06	ATP2A2, BIRC2, BIRC3, CTNNB1, GLI1, NFKBIZ, PDX1, PTGS2, SNAI1, SYN1, TNFSF10
CD40^b	Activated	2.02	3.22E−07	ANPEP, BIRC3, CCND2, CSF1, IL4R, ITGB1, LGALS3, MET, MMP14, MMP3, NEFH, NFKB1, NFKB2, PSMB9, PTGS2, TAPBP, TNFSF10, TP53AIP1, TRAF2, VEGFA
NFKB1^c		1.64	8.82E−09	ANKRD1, BIRC3, BTG2, CCND2, CSF1, EGFR, EGR1, ENPP2, GNAO1, JAG1, MMP10, MMP3, NFKB1, NFKB2, NMI, PTGS2, RELB, SDC4, SOD2, STAT1, TNFSF10, TRAF2, VEGFA
MAP3K14 (NIK)^b		1.59	3.09E−05	BIRC3, EGFR, NFKB1, PTEN, PTGS2, RELB, TNFSF10, TRAF3, YAP1
NFKBIA (IκBα)^a		1.14	4.71E−18	ANKRD1, BIRC2, BIRC3, BTG2, CCND2, CEBPB, CH25H, COL3A1, COL5A2, CSF1, CTNNB1, CYBA, DAG1, EIF4G2, ENPP2, ERAP2, GPR176, HMGA1, HOXB8, ITGB1, JUNB, KLF5, KRT18, MMP14, MMP3, NFKB1, NFKB2, NID1, PIK3R1, PTEN, PTGS2, RBP1, RELB, SDC4, SERPINE2, SGK1, SHH, SMAD4, SOD2, SORL1, TIMP3, TNFRSF10A, TNFSF10, TRAF2, VEGFA, VEGFC, WBP5, YAP1
NFKB2^a			4.18E−02	BIRC3, NFKB2, PTGS2, SOD2
HRAS^c		0.61	3.19E−16	ADM, AREG, ATP2A2, BTG2, CAV1, CCND2, CDKN2A, CDKN2B, CEBPB, COL18A1, COL3A1, COL5A2, CSF1, CTNNB1, EGFR, EGR1, EIF2D, FERMT2, FZD1, HNRNPA2B1, HOXB6, HRAS, HRASLS, IGFBP4, ITGAV, ITGB1, JUNB, KLF5, KRT18, MET, MMP14, MMP3, NID1, PDGFRA, PSMB9, PTEN, PTGS2, RARB, SERPINE2, SH3RF1, SIRPA, SMAD4, SNAI1, SOX5, SP3, SYN1, TIMP3, TNFRSF10A, TOM1, VEGFA, VIM, YAP1
STAT3^b		0.18	5.14E−09	ADM, AREG, CAT, CCND2, CDKN2A, CEBPA, CEBPB, COL3A1, EGR1, FERMT2, IFIH1, IL1R1, IL4R, JAG1, JUNB, MMP3, NFKB1, PEG10, PHLDA1, PMAIP1, PROK2, PSMB9, PTGS2, SERPINE2, SGK1, SHH, SNAI1, SOCS1, SOD2, STAT1, TFPI2, TNFSF10, VEGFA, VIM
CTNNB1 (β-catenin)^c^,^d		0.15	1.29E−12	ACTA2, ALCAM, ALDH1A1, ANXA1, BAMBI, CCND2, CDKN2A, CDKN2B, COL27A1, CRAT, CRIP1, CTNNB1, CYR61, DKK1, EGFR, EPHA5, FGF20, FLOT2, GAP43, GLI1, GNAO1, GREM1, HHIP, HOXA5, IGFBP2, IL1R1, ISL1, ITGB1, KLF5, LGALS3, MMP14, MMP3, NPTX1, NRCAM, POLR2A, POLR2E, PTGS2, SERPINE2, SGK1, SHH, SNAI1, SOX5, TIMP3, TJP1, VEGFA, VIM, YAP1
PTEN^c^,^d		−1.06	5.28E−09	ADM, ANGPT1, ANXA1, BTG2, CA12, CDK10, CDKN2A, CDKN2B, CTNNB1, DEGS1, EGFR, FES, IGFBP2, IL4R, JAG1, KLF5, KLF6, LGALS3, MET, MMP14, MMP3, NFKB1, PIK3R1, PTEN, PTGS2, SDC4, SHH, SMAD4, SMARCA4, TNFSF10, TOM1, VEGFA, VEGFC
EGR1^c		1.68	2.15E−08	ATP2A2, CAV1, CCND2, CSF1, EGFR, EGR1, JUNB, MMP14, NFKB1, PDX1, PTEN, PTGS2, SGK1, SNAI1, SOCS1, SOD2, SYN1, TNFSF10, VEGFA
PIK3R1^c^,^d		−0.05	3.51E−05	CCND2, PDGFRA, PDX1, PIK3R1, PTEN, PTGS2, SOD2, VEGFA, VEGFC
MAP3K1 (MEK)^a		1.19	3.96E−04	BIRC2, BIRC3, COL3A1, EGR1, MMP3, PTGS2, TNFRSF10A
MAPK1 (ERK2)^a		−0.58	8.90E−07	ANPEP, APOL6, CAV1, CTNNB1, DDX58, EGLN3, EGR1, FES, IFIH1, ITGAV, JUNB, L3MBTL1, LGALS3, NMI, PAQR6, PSMB9, PTGS2, SIRT1, SNAI1, SPRY4, STAT1, TJP1, TMEM158, TNFSF10, VIM
VEGFA^c		−1.90	7.38E−07	ADAMTS1, ANPEP, CAV1, CDKN2A, CYB5B, CYR61, EGR1, ETS2, FGFR1, GRB10, ID1, IGFBP4, ITGB1, JUNB, NME1, PTGS2, SOD2, TEK, TFPI2, VEGFA
ID1^c^,^d		−1.49	8.83E−04	BMI1, CDKN2A, EGR1, MMP14, SNAI1, VIM
TRAF3^b		−0.86	4.22E−05	ADM, BIRC3, EGFR, LRRC16A, MET, NFKB2, NFKBIA, PLBD1, RELB
ERBB4^c		1.39	3.11E−09	ACTA2, BTG2, CADM1, COL3A1, COL5A2, CTNNB1, EGFR, EGR1, ERBB4, GAP43, IGFBP4, NID1, PTGS2, SERPINE2, TIMP3
PRKCD^b		1.17	1.08E−04	BIRC2, BIRC3, CEBPB, GLI1, JUNB, KLF5, NFKB2, PTGS2, RELB, VEGFA
JUNB^c^,^d		0.82	2.40E−03	CAV1, CDKN2A, ITGAV, JUNB, MMP10, MMP3, RELB, SGK1, SNAI1

^{^a}

ChIPed by bcl3 in CT1-expressing cells with a FDR of >10.

^{^b}

Not ChIPed by bcl3 in CT1-expressing cells.

^{^c}

ChIPed by bcl3 in CT1-expressing cells with FDR of <10.

^{^d}

bcl3 peak overlaps ENCODE bcl3 peak.