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. 2010 Feb 4;5(2):e9063. doi: 10.1371/journal.pone.0009063

Table 2. Gene Ontology (Molecular Function) terms overrepresented (p<0.01) in the set of genes up- and down- regulated by TNFα.

A. Overrepresentation of down-regulated genes
GO_ID TERM NB_IN_REF NB_IN_SET pVAL
GO:0003677 DNA binding 3525 14 0.000379
GO:0005515 protein binding 8667 23 0.001096
GO:0016429 tRNA (adenine-N1-)-methyltransferase activity 1 1 0.001522
GO:0019767 IgE receptor activity 1 1 0.001522
GO:0004361 glutaryl-CoA dehydrogenase activity 1 1 0.001522
GO:0008326 site-specific DNA-methyltransferase (cytosine-specific) activity 1 1 0.001522
GO:0016426 tRNA (adenine)-methyltransferase activity 1 1 0.001522
GO:0019763 immunoglobulin receptor activity 2 1 0.00304
GO:0004105 choline-phosphate cytidylyltransferase activity 2 1 0.00304
GO:0051082 unfolded protein binding 202 3 0.003357
GO:0004032 aldehyde reductase activity 3 1 0.004553
GO:0004740 (pyruvate dehydrogenase (lipoamide)) kinase activity 4 1 0.006061
GO:0030414 protease inhibitor activity 270 3 0.0073
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity 87 2 0.007487
GO:0008168 methyltransferase activity 273 3 0.007515
GO:0019863 IgE binding 5 1 0.007565
GO:0016741 transferase activity, transferring one-carbon groups 277 3 0.007806
GO:0009008 DNA-methyltransferase activity 6 1 0.009065
GO:0005007 fibroblast growth factor receptor activity 6 1 0.009065
B. Overrepresentation of up-regulated genes
GO_ID TERM NB_IN_REF NB_IN_SET pVAL
GO:0016616 oxidoreductase activity, acting on the CH-OH group of 160 3 0.001262
donors, NAD or NADP as acceptor
GO:0016919 nardilysin activity 1 1 0.001353
GO:0050576 3-keto-steroid reductase activity 1 1 0.001353
GO:0004506 squalene monooxygenase activity 1 1 0.001353
GO:0048408 epidermal growth factor binding 1 1 0.001353
GO:0047747 cholate-CoA ligase activity 1 1 0.001353
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors 174 3 0.001597
GO:0004161 dimethylallyltranstransferase activity 2 1 0.002702
GO:0004337 geranyltranstransferase activity 2 1 0.002702
GO:0000247 C-8 sterol isomerase activity 2 1 0.002702
GO:0016491 oxidoreductase activity 1510 7 0.002977
GO:0004769 steroid delta-isomerase activity 3 1 0.004048
GO:0017147 Wnt-protein binding 3 1 0.004048
GO:0004505 phenylalanine 4-monooxygenase activity 3 1 0.004048
GO:0004090 carbonyl reductase (NADPH) activity 3 1 0.004048
GO_ID TERM NB_IN_REF NB_IN_SET pVAL
GO:0004146 dihydrofolate reductase activity 3 1 0.004048
GO:0004450 isocitrate dehydrogenase (NADP+) activity 4 1 0.00539
GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity 6 1 0.008064
GO:0016874 ligase activity 630 4 0.008635
GO:0042043 neurexin binding 7 1 0.009396