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

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

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