Table 2.

Gene ontology (GO) analysis for all significantly upregulated genes by chronic treatment with TNFα (2122 genes) or Il-1β (156 genes) using DAVID. Listed is the highest representative GO annotation term by false discovery rate (FDR) for each of the four highest clusters ranked by cluster enrichment score. Also listed is the total number of genes for each annotation category, the percentage of TNFα or Il-1β upregulated genes within this annotation, the fold-enrichment of this GO gene set, and the FDR corrected p values for each GO enrichment

Genes upregulated with TNFα treatment
Cluster	Cluster enrichment score	GO term	Total number of genes in category	% of TNFα upregulated genes in category	Fold enrichment	FDR
1	8.81	GO:0006952~defense response	118	5.98	1.75	1.77E−06
2	6.61	GO:0001817~regulation of cytokine production	50	2.54	2.52	2.02E−06
3	6.58	GO:0044421~extracellular region part	159	8.06	1.59	2.14E−06
4	5.57	GO:0043122~regulation of I-kappaB kinase/NF-kappaB cascade	32	1.62	2.73	4.43E−04
Genes Upregulated with IL-1β treatment
Cluster	Cluster enrichment score	GO Term	Total number of genes in category	% of IL-1β upregulated genes in category	Fold enrichment	FDR
1	4.77	GO:0006952~defense response	25	17.36	4.70	5.451E−07
2	3.30	GO:0019882~antigen processing and presentation	11	7.64	15.32	3.451E−06
3	2.39	GO:0050900~leukocyte migration	7	4.86	4.20	0.01
4	2.19	GO:0070011~peptidase activity, acting on L-amino acid peptides	12	8.33	2.68	6.12