Table 2 Biological processes and biochemical pathways enriched by genes exhibiting a diet by strain interaction
From: The effect of dietary fat intake on hepatic gene expression in LG/J AND SM/J mice
GO annotation term | GO annotation | Mus musculus genes FEFLIST (26185) | Number of genes in pathway | Number of genes expected | Over/under represented | P-value |
|---|---|---|---|---|---|---|
Biological Process | Â | Â | Â | Â | Â | Â |
immune system process | GO:0002376 | 2974 | 62 | 20.22 | + | 1.72×10-16 |
 antigen processing and presentation | GO:0019882 | 95 | 10 | 0.65 | + | 1.54×10-9 |
 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | GO:0002504 | 35 | 6 | 0.24 | + | 1.90×10-7 |
response to stimulus | GO:0050896 | 2486 | 52 | 16.9 | + | 1.01×10-13 |
 response to stress | GO:006950 | 547 | 13 | 3.72 | + | 1.08×10-4 |
 cellular defense response | GO:0006968 | 564 | 16 | 3.83 | + | 1.93×10-6 |
 response to toxin | GO:0009636 | 121 | 9 | 0.82 | + | 1.92×10-7 |
 signal transduction | GO:0007165 | 4858 | 52 | 33.02 | + | 3.68×10-4 |
 immune response | GO:0006955 | 900 | 16 | 6.12 | + | 4.75×10-4 |
Unclassified |  | 10946 | 39 | 74.41 | - | 1.81×10-8 |
 metabolic process | GO:0008152 | 9603 | 93 | 65.28 | + | 1.63×10-5 |
 primary metabolic process | GO:0044238 | 9122 | 91 | 62.01 | + | 6.03×10-6 |
 lipid metabolic process | GO:0006629 | 1266 | 24 | 8.61 | + | 6.06×10-6 |
 carbohydrate metabolic process | GO:005975 | 1038 | 19 | 7.06 | + | 9.55×10-5 |
 cellular process | GO:0009987 | 7133 | 69 | 48.49 | + | 5.51×10-4 |
 endocytosis | GO:0006897 | 604 | 14 | 4.11 | + | 7.65×10-5 |
 apoptosis | GO:0006915 | 1035 | 18 | 7.04 | + | 2.73×10-4 |
 developmental process | GO:0032502 | 3296 | 38 | 22.41 | + | 7.37×10-4 |
 system development | GO:0048731 | 2222 | 29 | 15.1 | + | 5.23×10-4 |
 transport | GO:0006810 | 3009 | 36 | 20.45 | + | 5.33×10-4 |
Biochemical Pathway | Â | Â | Â | Â | Â | Â |
Plasminogen activation cascade |  | 18 | 3 | 0.12 | + | 2.74×10-4 |
p53 pathway |  | 127 | 5 | 0.86 | + | 1.89×10-3 |
Angiogenesis |  | 193 | 6 | 1.31 | + | 2.22×10-3 |
Blood coagulation |  | 55 | 3 | 0.37 | + | 6.52×10-3 |
Integrin signalling pathway |  | 185 | 5 | 1.26 | + | 9.06×10-3 |
Androgen/estrogene/progesterone biosynthesis |  | 28 | 2 | 0.19 | + | 1.59×10-2 |
Ornithine degradation |  | 3 | 1 | 0.02 | + | 2.02×10-2 |
FAS signaling pathway |  | 38 | 2 | 0.26 | + | 2.80×10-2 |
Methylmalonyl pathway |  | 5 | 1 | 0.03 | + | 3.34×10-2 |
Xanthine and guanine salvage pathway |  | 6 | 1 | 0.04 | + | 4.00×10-2 |
p53 pathway feedback loops 2 |  | 51 | 2 | 0.35 | + | 4.77×10-2 |