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Table 1 Results of gene ontology analysis using the "biological process" annotation

From: Transcriptome analysis reveals a major impact of JAK protein tyrosine kinase 2 (Tyk2) on the expression of interferon-responsive and metabolic genes

GO category # genes ER NC p-value
(A)     
humoral defense mechanism sensu Vertebrata 11 1.58 4.3 0
antigen presentation 11 1.54 4.02 0
defense response 46 1.34 2.72 0
immune response 102 1.28 2.31 0
positive regulation of transcription     
DNA-dependent 13 1.19 1.65 0.0013
regulation of apoptosis 45 1.11 0.94 0.0005
protein ubiquitination 78 1.06 0.58 0.0049
protein modification 71 1.06 0.57 0
transcription 449 1.04 0.34 0
regulation of transcription DNA.dependent 586 1.03 0.29 0
transport 576 0.97 -0.29 0.0002
electron transport 138 0.95 -0.49 0.002
metabolism 151 0.92 -0.8 0
sodium ion transport 22 0.88 -1.2 0.0025
biosynthesis 24 0.87 -1.26 0.0009
fatty acid biosynthesis 15 0.85 -1.57 0.0011
lipid biosynthesis 34 0.83 -1.77 0
steroid biosynthesis 20 0.83 -1.79 0
cholesterol biosynthesis 12 0.79 -2.21 0
sterol biosynthesis 13 0.77 -2.5 0
(B)     
inflammatory response 46 2.24 7.55 0
chemotaxis 30 2 6.48 0
immune response 102 1.93 6.18 0
sensory perception 42 1.64 4.66 0
defense response to bacteria 11 1.63 4.61 0.0001
defense response 46 1.37 2.97 0
cell surface receptor linked signal transduction 32 1.28 2.28 0.001
sensory perception of smell 70 1.25 2.08 0
cell proliferation 42 1.24 2.03 0.0008
signal transduction 222 1.21 1.79 0
regulation of apoptosis 45 1.2 1.73 0
G-rotein coupled receptor protein signaling pathway 166 1.15 1.32 0
regulation of transcription 119 1.1 0.87 0
regulation of transcription DNA.dependent 586 1.04 0.38 0
electron transport 138 0.87 -1.26 0
metabolism 151 0.82 -1.91 0
lipid metabolism 59 0.79 -2.21 0
lipid biosynthesis 34 0.77 -2.49 0
fatty acid metabolism 32 0.71 -3.15 0
(C)     
negative regulation of progression through cell cycle 26 1.17 0.95 0.0022
anti apoptosis 30 1.17 0.92 0.0015
metabolism 151 0.92 -0.47 0.0009
protein biosynthesis 180 0.92 -0.52 0
cell proliferation 42 0.87 -0.8 0.0021
fatty acid metabolism 32 0.85 -0.95 0.0015
rRNA processing 29 0.85 -0.97 0.0019
lipid biosynthesis 34 0.84 -1.02 0.0004
steroid biosynthesis 20 0.83 -1.09 0.0037
sterol biosynthesis 13 0.8 -1.34 0.0039
cholesterol biosynthesis 12 0.79 -1.43 0.003
  1. Within the "biological process" annotation, gene classes (412 in total) were separately contrasted with all other classes using t- tests on standardized coefficients. (A) Basal differences between genotypes, (B) LPS induction in Wt, and (C) differences between genotypes in LPS induction (genotype by treatment interaction). ER, approximate mean expression ratio, NC, mean normed coefficients.