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Table 4 Pathways enriched in secondary Hoxa1 interactors

From: Protein interactions of the transcription factor Hoxa1

Pathway name ID* Obs$ Odds ratio£ FDRμ Corr FDR§ Source Gene symbols Entrez gene IDs
RXR and RAR hetrodimerization with other nuclear receptor pc926 2 24,83 2,00E-05 2,40E-03 NCI-Nature FAM120B,NR1H2 84498,7376
Cell adhesion molecules (CAMs) - Homo sapiens (human) hsa04514 2 19,70 9,00E-05 1,35E-02 KEGG CLDN2,PVRL2 9075,5819
Gap junction - Homo sapiens (human) hsa04540 2 16,59 8,00E-05 1,20E-02 KEGG GNAI2,PDGFRB 2771,5159
Signaling events mediated by PTP1B pc948 4 12,72 1,00E-05 1,20E-03 NCI-Nature CRK,SPRY2,TRPV6,PDGFRB 1398,10253,55503,5159
Retinoic acid receptors-mediated signaling pc960 3 10,19 2,10E-04 2,52E-02 NCI-Nature NR1H2,NRIP1,FAM120B 7376,8204,84498
Integrins in angiogenesis pc989 3 10,04 3,40E-04 4,08E-02 NCI-Nature CDKN1B,SPP1,VCL 1027,6696,7414
Down-stream signal transduction pc690 2 8,28 5,00E-05 3,14E-02 Reactome PDGFRB,NCK2 5159,8440
Signaling by PDGF pc876 2 8,28 5,00E-05 3,14E-02 Reactome PDGFRB,NCK2 5159,8440
Toll-like receptor signaling pathway - Homo sapiens (human) hsa04620 3 7,54 3,20E-04 4,80E-02 KEGG TRAF6,TOLLIP,SPP1 7189,54472,6696
Homologous recombination - Homo sapiens (human) hsa03440 2 7,18 1,40E-04 2,10E-02 KEGG TOP3B,RAD54B 8940,25788
LPA receptor mediated events pc1042 4 7,07 1,30E-04 1,56E-02 NCI-Nature BIRC2,TRIP6,TRAF6,CRK 329,7205,7189,1398
Focal adhesion - Homo sapiens (human) hsa04510 8 6,55 3,00E-05 4,50E-03 KEGG SPP1,VCL,VASP,CRK,PDGFRB,BIRC2,CCND3,PAK7 6696,7414,7408,1398,5159,329,896,57144
TCR signaling in naive CD4+ T cells pc1031 4 6,54 3,00E-04 3,60E-02 NCI-Nature BIRC2,TRAF6,GRAP2,TRPV6 329,7189,9402,55503
Axon guidance - Homo sapiens (human) hsa04360 5 6,50 1,40E-04 2,10E-02 KEGG GNAI2,PAK7,NTN4,ABLIM1,NCK2 2771,57144,59277,3983,8440
TCR signaling in naive CD8+ T cells pc997 4 6,34 3,80E-04 4,56E-02 NCI-Nature TRAF6,GRAP2,TRPV6,BIRC2 7189,9402,55503,329
Lysine degradation - Homo sapiens (human) hsa00310 3 6,28 1,00E-04 1,50E-02 KEGG OGDH,AASDHPPT,EHMT2 4967,60496,10919
IGF1 pathway pc1041 3 6,26 3,60E-04 4,32E-02 NCI-Nature CRK,NCK2,YWHAE 1398,8440,7531
p75(NTR)-mediated signaling pc978 5 6,02 2,60E-04 3,12E-02 NCI-Nature YWHAE,TRAF6,BIRC2,RTN4,LINGO1 7531,7189,329,57142,84894
Proteogylcan syndecan-mediated signaling events pc1045 5 5,53 2,20E-04 2,64E-02 NCI-Nature BSG,HGS,CRK,SPRY2,SPP1 682,9146,1398,10253,6696
Syndecan-1-mediated signaling events pc974 3 5,46 1,60E-04 1,92E-02 NCI-Nature BSG,CRK,HGS 682,1398,9146
Plasma membrane estrogen receptor signaling pc1048 6 4,07 3,60E-04 4,32E-02 NCI-Nature CRK,SLC9A1,IRF4,NCK2,YWHAE,TRAF6 1398,6548,3662,8440,7531,7189
  1. * pathway identifier.
  2. $ number of Hoxa1 interactors belonging to the corresponding pathway.
  3. £ the odds ratio represents the enrichment of the corresponding pathway, an odds ratio of 10 meaning that the considered pathway is observed 10 times more than expected at random.
  4. μfalse discovery rate as computed through the simulation.
  5. §corrected false discovery rate accounting for multiple testing.