OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif

Drawid, Amar; Gupta, Nupur; Nagaraj, Vijayalakshmi H; Gélinas, Céline; Sengupta, Anirvan M

doi:10.1186/1471-2105-10-208

Table 1 Enriched pathways, functions and diseases

From: OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif

Pathway/Function/Disease	Gene Symbols
NF-κB Signaling	NFKB2, CD40, IL1F9, IKBKB, RRAS, TNFAIP3, BCL3, TLR7, TRAF5, NFKBIB, NFKB1, LTA, PIK3C3, NFKBIA, RELB, BTRC, PIK3R2, ZAP70, TRAF3, IL1RN*, PLCG2, MAP3K8
Glucocorticoid Receptor Signaling	VCAM1, ICAM1, MED1, SMAD3, IKBKB, RRAS, MAPK12, BCL3, IL13, CCL5, NFKBIB, NFKB1, IL8, PIK3C3, NFKBIA, NR3C1, STAT1, CXCL3, CREB1, PIK3R2, JAK3, SELE, IL1RN, IL6*
Antigen Presentation Pathway	B2M, PSMB9, HLA-A, CD74, HLA-B, HLA-DQA1, TAPBP
Acute Phase Response Signaling	SAA1, IL1F9, RBP1, IKBKB, RRAS, MAPK12, BCL3, SERPINA3, NFKBIB, CFB, NFKBIA, NR3C1, PIK3R2, NOLC1, SAA2, SOCS2, IL1RN, IL6*
B Cell Receptor Signaling	IKBKB, RRAS, MAPK12, BCL3, NFKBIB, CALML5, NFATC1, PTPN6, NFKBIA, PIK3C3, CREB1, MAP3K11, PIK3R2, PLCG2, MAP3K8
Death Receptor Signaling	NFKBIA, BIRC3, DIABLO, IKBKB, BCL3, TANK, NFKBIB, TNFSF15*
Apoptosis Signaling	NFKBIA, BIRC3, DIABLO, IKBKB, RRAS, BCL3, MAPK6, TP53*, NFKBIB, RPS6KA1, PLCG2, MAP3K8
Cell Cycle: G1/S Checkpoint Regulation	BTRC, SMAD3, SIN3A, TP53*, HDAC8, E2F6
Chemokine Signaling	CCL4, RRAS, CCR3, MAPK12, CCL5, PLCG2, CALML5
T Cell Receptor Signaling	NFATC1, PIK3C3, NFKBIA*, IKBKB, RRAS, PIK3R2, ZAP70, CALML5
Notch Signaling	DLL1, NOTCH2, RBPJ, MAML2
P53 Signaling	BBC3, PIK3C3, SIRT1, PPP1R13B, MED1, PIK3R2, TP53*
Xenobiotic Metabolism Signaling	IL4I1, SULT1C2, MED1, RRAS, MAPK12, NFKB1, NFKB2, GSTP1, PIK3C3, PPP2CB, ALDH3B2, EIF2AK3, PIK3R2, NFE2L2, IL6, IL1RN*, GSTA5
Neurotrophin/TRK Signaling	PIK3C3, CREB1, RRAS, PIK3R2, RPS6KA1
Protein Ubiquitination Pathway	UBE2H, UBE2D3, B2M, UBE2M, BIRC3, BTRC, PSMB9, HLA-A, HLA-B
Skeletal and Muscle Development and Function	CD40, CSF1, CXCL11, DLL1, IKBKB, IL6, IL13, IL1RN, MED1, NFATC1, NFKB1, NFKB2, NFKBIA, RBPJ, SMAD3, STAT1, VCAM1, WNT10B*
Infection of Virus	CCL4, CCL5, CLEC4M, DEFA1, ICAM1, IL13, IRF8, XPO1
Cancer	ACACA, AIM2, B2M, BBC3, BCL2L10, BIRC3, BTRC, C6ORF66, CARD8, CD40, CREB1, CTGF, CYLD, DBC1, DIABLO, DLL1, DPP4, DUT, EGR2, EIF2AK3, GNB1, GNB2L1, HINT1, HUWE1, IER3, IFNB1, IGFBP6, IL6, IL8, IL13, IL1RN, IRF1, IRF8, ITGA5, LCN2, LTA, LTB, MAML2, MAP3K11, MAPK12, MEN1, MIA, MSX1, MYB, NFKB1, NFKB2, NFKBIA, NFKBIZ, NR3C1, OAS3, PLCG2, PPP1R13B, PPP5C, PTPN6, RBM17, REL, RHOC, RPS6KA1, RUNX1T1, SMPD2, STAT1, THOC1, TNFAIP3, TNFSF13, TP53, TRAF3, TWIST1*
Rheumatoid Arthritis	ACAN, ACTA1, ADAMTS7, B2M, BLR1, CARD8, CCL1, CCL4, CCL5, CCL19, CD40, CD69, CD70, CD74, CD83, CD86, CD274, CFB, CXCL1, CXCL2, CXCL3, CXCL5, CXCL6, CXCL10, DEFA1, DPP4, GP1BA, HLA-A, HLA-DQA1, HPRT1, ICAM1, IFNB1, IL6, IL8, IL13, LTA, LTB, MAPK12, NFKB1, NFKBIA, NR3C1, PSMB9, SAA1, SAA2, TNFAIP3, TNFRSF13B, TNFSF15, TP53, TPM2, VIM, WNT10B
Experimental Autoimmune Encephalomyelitis	B2M, CD40, CD86, CXCL10, DPP4, HLA-DQA1, IFNB1, IKBKB, IL6, LTA, LTB, NR3C1, REL, STAT1

Selected cellular pathways, biological functions and diseases in which our predicted NF-κB targets were over-represented are shown. The associated predicted NF-κB targets are represented by official human gene symbols. Genes containing κB sites with predicted occupancy probability greater than 0.5 were used in this analysis. Please see Additional file 5 for the complete list. Genes known in the literature to be regulated by NF-κB (although not necessarily directly) [38] are denoted with *.

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ISSN: 1471-2105

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