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Table 2 KEGG pathway analysis for differentially expressed genes between JS1 and JS2 cells and the key regulatory genes

From: Transcriptomic analysis of the effects of Toll-like receptor 4 and its ligands on the gene expression network of hepatic stellate cells

Pathway ID Pathway term Enrichment (+, up; −, down) P value No. of DifGenes Gene-act-network core genes (degree >5) Co-expression network core genes (Dif-degree >5)
path:mmu04115 p53 signaling pathway +1.971 0.013637 18 Ccnd1, Igf1 Apaf1
path:mmu0415 mTOR signaling pathway +1.934 0.030489 14 Rps6ka1, Pik3r3, Mapk1, Igf1, Braf, Ins2 Rps6ka1
path:mmu04621 NOD-like receptor signaling pathway +1.857 0.0298641 16 Mapk1, Mapk12, Map3k7 Tab3, Birc2
path:mmu04630 Jak-STAT signaling pathway +1.511 0.049774 25 Jak2,Stat5b,Stat5a, Il6st, Pik3r3, Akt3,Ptpn11,Stat3,Ifnar1,Stat6, Stat2 Jak2, Stat5a, Stat5b, Il6st, Grb2, Il20rb, Socs5
path:mmu04062 Chemokine signaling pathway +1.489 0.042555 29 Jak2,Prkacb, Gsk3b, Mapk1, Kras, Plcb3, Gnai3, Cdc42, Braf,Stat5b, Stat3, Shc4, Pard3, Il11ra1 Jak2, Prkacb , Gsk3b, Grb2
path:mmu04510 Focal adhesion +1.469 0.025892 39 Pdgfra, Pdgfrb, Prkca, Gsk3b, Fn1, Mapk1, Itga11, Igf1r, Jun,Akt3, Igf1, Tnc, Braf, Col5a1, Col3a1, Col1a2, Col1a1, Thbs3, Thbs1, Col6a2, Col6a1, Col4a6, Tln2, Ugdh Pdgfra, Pdgfrb, Prkca, Gsk3b, Fn1, Grb2, Birc2, Ppp1cb
path:mmu05200 Pathways in cancer +1.350 0.032167 57 Pdgfra, Pdgfrb, Prkca, Grb2, Gsk3b, Fn1, Pik3r3, Egfr, Mapk1, Kras, Jun, Akt3, Igf1, Braf, Stat5b, Stat5a, Figf, Cdk4, Stat3, Pias1, Mdm2 Pdgfra, Pdgfrb, Prkca, Gsk3b, Fn1, Mmp2, Flt3l, Birc2, Brca2, Appl1, Casp3, Fzd1, Msh2
path:mmu04514 Cell adhesion molecules (CAMs) −1.493 0.046196 28 H2-M2, LOC547349, H2-Q7, H2-Q2, Itgb7, Sdc3, LOC100044874, H2-M3, H2-T23, H2-T10, H2-K1, H2-Q8,H2-Q6, H2-Q10, Itgb6, H2-D1, Sdc2 H2-M2, H2-Q7, Itgb7, LOC547349, H2-Q2, Sdc3, F11r, Madcam1, Selp
path:mmu04145 Phagosome −1.640 0.006056 41 H2-M2, H2-Q2, H2-Q7, LOC547349, LOC100044874, H2-M3, H2-T23, H2-T10, H2-K1, H2-Q8, H2-Q6, H2-Q10, H2-D1, Itgb5, Itgb3, Itga5, Actg1 H2-M2, H2-Q2, H2-Q7, LOC547349, Atp6v0b, Atp6v1h, Atp6v1e1, Sec61b, Atp6v0c
path:mmu04360 Axon guidance −1.653 0.013723 33 Hras1, Mapk3, Ptk2, Nras, Tapbp Hras1, Sema3a, Sema4f, Ephb3, Nfatc2
path:mmu04612 Antigen processing and presentation −1.886 0.012941 21 H2-M2, H2-Q2, H2-Q7, LOC547349, LOC100044874, H2-M3, H2-T23, H2-T10, H2-K1, H2-Q6, H2-Q8, H2-Q10, H2-D1, Tapbp H2-M2, H2-Q2, H2-Q7 , LOC547349
  1. Note: Genes that are identified to be key regulatory factors by both gene-act-net work and co-expression network analysis (degree or difference degree >5) are marked in bold and italic font