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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
  1. 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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