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

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

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

ISSN: 1755-1536