Text Mining-Based Drug Discovery in Osteoarthritis

Table 2

Summary of KEGG pathways gene set enrichment analysis.

Pathways	Genes in query set	Total genes in genome	Percentage (%)	value	Genes
TNF signaling pathway	9	108	0.267857	1.73E-10	CASP3, TNFRSF1B, IL6, TNF, CCL2, PTGS2, RELA, MMP9, MAPK8
NOD-like receptor signaling pathway	7	166	0.208333	5.53E-09	IL6, TNF, CCL2, RELA, CXCL8, MAPK8, NLRP3
Pathways in cancer	11	515	0.327381	1.92E-08	CASP3, IL6, PTGS2, RELA, MMP9, VEGFA, TP53, CXCL8, MAPK8, BCL2L1, STAT3
Apoptosis	6	135	0.178571	5.33E-07	CASP3, TNF, RELA, TP53, BCL2L1, NGF
NF-kappa B signaling pathway	6	93	0.178571	2.91E-06	TNF, PTGS2, RELA, CXCL8, BCL2L1, CD40
Toll-like receptor signaling pathway	6	102	0.178571	7.74E-06	IL6, TNF, RELA, CXCL8, MAPK8, CD40
Amyotrophic lateral sclerosis (ALS)	5	50	0.14881	8.84E-06	CASP3, TNFRSF1B, TNF, TP53, BCL2L1
Inflammatory bowel disease (IBD)	5	62	0.14881	2.38E-05	IL6, TNF, RELA, IL10, STAT3
Cytokine-cytokine receptor interaction	7	263	0.208333	3.37E-05	TNFRSF1B, IL6, TNF, CCL2, CXCL8, CD40, IL10
Adipocytokine signaling pathway	5	69	0.14881	3.40E-05	TNFRSF1B, TNF, RELA, MAPK8, STAT3

To make sure that only the most enriched annotations were selected, a value cutoff () was set. Among the most significantly enriched pathway annotations above the cutoff, those most relevant to OA pathology based on the available literature and research were selected. A total of 10 pathways were picked out from the analysis of enriched pathway annotations.