Table 6.
Function enrichment analysis for genes in the PPI network.
| Term | p value | Genes | |
|---|---|---|---|
| KEGG | Hedgehog signaling pathway | 1.84E − 03 | BOC; PTCH2; GLI2; CDON |
| Basal cell carcinoma | 5.36E − 03 | FZD2; FZD5; PTCH2; GLI2 | |
| Other types of O-glycan biosynthesis | 2.47E − 02 | POMT2; LFNG | |
| Mannose type O-glycan biosynthesis | 2.68E − 02 | B3GALNT2; POMT2 | |
| Hippo signaling pathway | 3.38E − 02 | TGFB2; FZD2; FZD5; RASSF4; GLI2 | |
| Pathways in cancer | 3.60E − 02 | RET; DLL4; GSTM2; TGFB2; FZD2; FZD5; PTCH2; BRCA2; PGF; GLI2; ADCY5 | |
| Mucin type O-glycan biosynthesis | 4.66E − 02 | GALNT6; ST3GAL2 | |
| Cytokine-cytokine receptor interaction | 4.72E − 02 | TGFB2; CCL7; TNFRSF19; ACKR3; INHBB; CCL19; RELT | |
| MAPK signaling pathway | 4.80E − 02 | TGFB2; FLT1; ANGPT2; CACNA2D2; CACNA1A; DUSP9; PGF | |
| BioCarta | Rho cell motility signaling pathway_Homo sapiens_h_rhoPathway | 4.93E − 02 | CACNA1A; ASAP2 |
| Reactome | GLI proteins bind promoters of Hh responsive genes to promote transcription_Homo sapiens_R-HSA-5635851 | 4.63E − 05 | BOC; PTCH2; GLI2 |
| Hedgehog 'on' state_Homo sapiens_R-HSA-5632684 | 3.77E − 04 | BOC; PTCH2; IQCE; DZIP1; GLI2; CDON | |
| Signaling by Hedgehog_Homo sapiens_R-HSA-5358351 | 8.44E − 04 | PTCH2; BOC; IQCE; DZIP1; CDON; GLI2; ADCY5 | |
| Signal Transduction_Homo sapiens_R-HSA-162582 | 1.50E − 02 | RET; AMER1; FLT1; WIPF3; USP34; ATP2A1; KALRN; LTB4R; THBS4; GLI2; ADCY5; LFNG; SYDE2; SPRED3; DLL4; HCAR1; CCL7; KIF5A; BOC; GRB10; S1PR3; CCL19; S1PR2; SRGAP2; TAS2R5; CDON; PDK1; LINGO1; FZD2; FZD5; PTCH2; IQCE; ARHGEF18; INHBB; DUSP9; PGF; ACKR3; CENPO; DZIP1 | |
| GO BP | Embryonic digestive tract development (GO:0048566) | 1.36E − 03 | TGFB2; PKDCC; GLI2 |
| Digestive tract development (GO:0048565) | 1.44E − 03 | TGFB2; PKDCC; GATA2; GLI2 | |
| Spinal cord dorsal/ventral patterning (GO:0021513) | 1.80E − 03 | DLL4; GLI2 | |
| Renal system development (GO:0072001) | 4.50E − 03 | TGFB2; SIX1; LRP4; GLI2 | |
| Kidney development (GO:0001822) | 5.67E − 03 | TGFB2; SIX1; LRP4; GLI2 | |
| Axon guidance (GO:0007411) | 8.94E − 03 | RET; KIF5C; KIF5A; GRB10; PLXNA2; GLI2 | |
| Odontogenesis (GO:0042476) | 1.14E − 02 | TGFB2; AQP5; GLI2 | |
| Branching morphogenesis of an epithelial tube (GO:0048754) | 1.29E − 02 | DLL4; SIX1; GLI2 | |
| Axonogenesis (GO:0007409) | 1.31E − 02 | RET; LINGO1; KIF5C; KIF5A; GRB10; DSCAML1; GLI2 | |
| Dorsal/ventral pattern formation (GO:0009953) | 2.06E − 02 | DSCAML1; GLI2 | |
| Embryonic skeletal system development (GO:0048706) | 2.26E − 02 | SIX1; DSCAML1 | |
| Cell morphogenesis involved in neuron differentiation (GO:0048667) | 2.41E − 02 | LINGO1; CDHR1; LRP4; DSCAML1 | |
| Embryonic skeletal system morphogenesis (GO:0048704) | 2.47E − 02 | SIX1; DSCAML1 | |
| Positive regulation of nucleic acid-templated transcription (GO:1903508) | 2.60E − 02 | RET; NFE2; AFAP1L2; FZD2; MYCN; MYRF; NFE2L3; SIX1; PBX4; BRCA2; GLI2 | |
| Heart development (GO:0007507) | 2.66E − 02 | TGFB2; TCAP; GATA2; GLI2; TBX2 | |
| Endocrine system development (GO:0035270) | 3.62E − 02 | SIX1; GLI2 | |
| Neuron projection morphogenesis (GO:0048812) | 3.69E − 02 | LINGO1; CNTNAP1; LRP4; SRGAP2; DSCAML1 | |
| Skeletal system morphogenesis (GO:0048705) | 4.93E − 02 | SIX1; DSCAML1 | |
| GO MF | Transcription regulatory region sequence-specific DNA binding (GO:0000976) | 5.77E − 03 | NFE2; CUX1; NFE2L3; ARID3A; ARID3B; GATA2; ZBED6; HOXD9; ETV5 |
| RNA polymerase II regulatory region DNA binding (GO:0001012) | 7.67E − 03 | CUX1; ARID3A; ARID3B; GATA2; ZBED6; HOXD9; ETV5 | |
| Guanylate kinase activity (GO:0004385) | 8.90E − 03 | MPP2; MAGI3 | |
| Growth factor receptor binding (GO:0070851) | 2.03E − 02 | LINGO1; ESM1; TNK2; PGF | |
| Protein tyrosine kinase activity (GO:0004713) | 2.53E − 02 | RET; PKDCC; FLT1; CUX1; TNK2 | |
| Nucleotide kinase activity (GO:0019201) | 2.68E − 02 | MPP2; MAGI3 | |
| Epidermal growth factor receptor binding (GO:0005154) | 3.37E − 02 | LINGO1; TNK2 | |
| RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977) | 3.45E − 02 | MYCN; CUX1; SIX1; ARID3A; ARID3B; GATA2; ZBED6; HOXD9; ETV5; TBX2 | |
| WW domain binding (GO:0050699) | 4.39E − 02 | NFE2; TNK2 |
PPI, protein-protein interaction; KEGG, Kyoto Encyclopedia of Genes and Genomes; GO, Gene Ontology; BP, biological process; MF, molecular function.