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