Integrated network analysis of transcriptomic and protein-protein interaction data in taurine-treated hepatic stellate cells

Table 1 Gene ontology enrichment results of differentially expressed genes

GO	Count	P-value	Description
Enriched GO biological process of DEGs
GO:0007165	52	0.001	Signal transduction
GO:0006508	24	0.015	Proteolysis
GO:0008283	18	0.03	Cell proliferation
GO:0070374	13	0.004	Positive regulation of ERK1 and ERK2 cascade
GO:0001666	12	0.009	Response to hypoxia
GO:0018108	10	0.029	Peptidyl-tyrosine phosphorylation
GO:0001501	9	0.04	Skeletal system development
GO:0050907	8	0.018	Detection of chemical stimulus involved in sensory perception
GO:0002576	8	0.026	Platelet degranulation
GO:0006302	7	0.011	Double-strand break repair
GO:0050731	7	0.028	Positive regulation of peptidyl-tyrosine phosphorylation
GO:0097191	6	0.006	Extrinsic apoptotic signaling pathway
GO:0007269	6	0.014	Neurotransmitter secretion
GO:0043406	6	0.025	Positive regulation of MAP kinase activity
Enriched GO chemical component of DEGs
GO:0005886	148	0.000	Plasma membrane
GO:0005887	66	0.000	Integral component of plasma membrane
GO:0005576	59	0.027	Extracellular region
GO:0009897	13	0.017	External side of plasma membrane
GO:0005604	7	0.023	Basement membrane
GO:0098793	6	0.033	Presynapse
Enriched GO molecular function of DEGs
GO:0042802	33	0.010	Identical protein binding
GO:0005509	32	0.009	Calcium ion binding
GO:0004888	14	0.007	Transmembrane signaling receptor activity
GO:0005516	12	0.016	Calmodulin binding
GO:0005215	12	0.025	Transporter activity
GO:0004222	9	0.013	Metalloendopeptidase activity
GO:0004713	9	0.031	Protein tyrosine kinase activity
GO:0008237	8	0.007	Metallopeptidase activity
GO:0002020	8	0.022	Protease binding
GO:0003707	6	0.019	Steroid hormone receptor activity
GO:0008236	6	0.030	Serine-type peptidase activity
GO:0003705	6	0.036	Transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0001540	5	0.014	Hormone binding
GO:0001206	4	0.002	Peptidoglycan binding

GO: Gene ontology; DEGs: Differentially expressed genes.

Table 2 Cluster of differentially expressed genes in the protein-protein interaction network

Cluster	Score	Nodes	Edges	Genes
1	7.818	12	43	TCOF1, MMRN1, TGFB1, FIGF, VEGFB, TIMP3, FGB, EGFR, F7, EGF, BDNF, MMP9
2	5.556	10	25	ESR1, DNAH8, MMP2, JAK2, SRC, ESR2, CYP19A1, GPER, NPS, NR3C1
3	4.286	29	60	NPSR1, PIKFYVE, KLHL11, KBTBD8, PMS2, XRCC4, RCVRN, TAS2R9, CACNA1B, RAD52, OGN, NPFFR2, WRN, GRPR, CABP2, RYR1, ZBTB16, ASB5, CAMK2D, BGN, RAD51B, CCL25, UBE2V1, HECW2, OPRM1, PRKACB, TAB1, HTR5A, ADCY4
4	4	4	6	ALDH4A1, GCSH, DBT, OGDH
5	4	4	6	THSD7B, ADAMTSL1, ADAMTS1, THSD1
6	4	4	6	C2CD3, NPHP1, HAUS6, HAUS1
7	3.429	8	12	RASL10A, FRYL, LRRC69, DIRAS1, ERAS, RAP1A, RANBP2, OMG
8	3	3	3	RGPD1, NUTF2, KPNA5
9	3	3	3	UTY, ZFY, CECR2
10	3	3	3	TBX5, CFC1, GJA5
11	3	3	3	SYCP2, POT1, HIST1H2BD