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Table 3 KEGG pathway analysis for differentially expressed genes in JS1 cells with or without LPS treatments 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

Path Path Term Enrichment (+, up; −, down) P value No. of genes Gene-act-network core genes (degree >3) Co-expression network core genes (Dif-degree >3)
path:mmu00010 Glycolysis/gluconeogenesis +3.226 0.002679 10 Hk1 Gm5506, Tpi1, Ldha
path:mmu03420 Nucleotide excision repair +3.110 0.008222 8 / Rfc2, Ercc1, Cdk7
path:mmu03040 Spliceosome +2.030 0.013765 15 / Ddx39b, Snrpb, Rpa2, Prpf19, Ppie, Hnrnpa3
path:mmu04620 Toll-like receptor signaling pathway +2.224 0.018448 11 Mapk9, Mapk14 Mapk9, Mapk14
path:mmu04722 Neurotrophin signaling pathway +1.965 0.021031 14 Mapk14, Cdc42 Mapk14
path:mmu05320 Autoimmune thyroid disease +2.589 0.028615 7 H2-Q2, H2-Q10,LOC100044874,H2-T10,H2-Bl H2-Q2
path:mmu03030 DNA replication +2.757 0.032638 6 / Pola2
path:mmu04070 Phosphatidylinositol signaling system −3.880 0.003976 7 Prkca, Pik3r3 Prkca
path:mmu04530 Tight junction −2.431 0.025024 8 Prkca, Myl9 /
path:mmu04120 Ubiquitin mediated proteolysis −2.231 0.028651 9 Map3k1 Map3k1, Herc1, Prkca, Ubr5
  1. Note: Genes that are identified to be key regulatory factors by both gene-act-network and co-expression network analysis (degree or difference degree >3) are marked in bold and italic font