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

Table 4 KEGG pathway analysis for differentially expressed genes in JS1 cells with or without HMGB1 treatments and the key regulatory genes

Path	Path term	Enrichment (+, up; −, down)	P value	No. of genes	Gene-act-network core genes (degree >3)	Co-expression network Dif-degree >3
path:mmu03410	Base excision repair	+4.857	0.001406	7	/	Nthl1, Mpg
path:mmu00480	Glutathione metabolism	+3.001	0.022114	6	*Gpx4,Gstt2*,Gstp1,Mgst3,Gstp2	*Gstt2, Gpx4, Odc1*
path:mmu00982	Drug metabolism—cytochrome P450	+2.805	0.028716	6	*Gstt2,Cyp2e1,* Mgst3,Gstp1	*Gstt2, Cyp2e1*
path:mmu04120	Ubiquitin-mediated proteolysis	−2.378	0.003899	15	Traf6	Ube2n, Uba3, Herc1
path:mmu04150	mTOR signaling pathway	−3.012	0.014331	7	Mapk1	Rps6ka3
path:mmu05200	Pathways in cancer	−1.622	0.030471	22	Igf1r,Prkca,Mapk1,Ptk2	Rala, E2f3, Foxo1
path:mmu04622	RIG-I-like receptor signaling pathway	−2.342	0.041959	7	Traf6	Cyld

Note: Genes that are identified to be key regulatory factors by both gene-act-network analysis and co-expression network analysis (degree or difference degree >3) are marked in bold and italic font

ISSN: 1755-1536