Table 2.
Overrepresented Gene Ontology classes in the gastrocnemius as compared to the quadriceps
| GO ID | GO class | N | Raw Score | FDR |
|---|---|---|---|---|
| GO:0001974 | blood vessel remodeling | 15 | 1.99 | 2.39E-10 |
| GO:0006776 | vitamin A metabolic process | 15 | 1.92 | 9.95E-11 |
| GO:0051705 | behavioral interaction between organisms | 18 | 1.63 | 3.89E-04 |
| GO:0006775 | fat-soluble vitamin metabolic process | 20 | 1.57 | 4.17E-04 |
| GO:0048705 | skeletal morphogenesis | 17 | 1.41 | 8.14E-04 |
| GO:0009855 | determination of bilateral symmetry | 31 | 1.30 | 5.97E-11 |
| GO:0003007 | heart morphogenesis | 29 | 1.28 | 8.53E-11 |
| GO:0014033 | neural crest cell differentiation | 31 | 1.28 | 3.98E-10 |
| GO:0006936 | muscle contraction | 69 | 1.19 | 1.49E-10 |
| GO:0006937 | regulation of muscle contraction | 25 | 1.19 | 7.35E-04 |
| GO:0043010 | camera-type eye development | 56 | 1.14 | 7.02E-11 |
| GO:0007368 | determination of left/right symmetry | 30 | 1.14 | 8.02E-04 |
| GO:0048762 | mesenchymal cell differentiation | 38 | 1.13 | 9.19E-11 |
| GO:0008016 | regulation of heart contraction | 34 | 1.13 | 3.23E-04 |
| GO:0060047 | heart contraction | 41 | 1.11 | 1.09E-10 |
| GO:0007498 | mesoderm development | 44 | 1.06 | 1.33E-10 |
| GO:0001654 | eye development | 82 | 1.03 | 7.46E-11 |
| GO:0048592 | eye morphogenesis | 37 | 1.02 | 6.97E-04 |
| GO:0006766 | vitamin metabolic process | 56 | 1.01 | 6.28E-11 |
| GO:0009952 | anterior/posterior pattern formation | 86 | 0.96 | 4.59E-11 |
| GO:0016055 | Wnt receptor signaling pathway | 107 | 0.94 | 4.98E-11 |
| GO:0042445 | hormone metabolic process | 71 | 0.92 | 1.71E-04 |
| GO:0048771 | tissue remodeling | 104 | 0.92 | 1.71E-10 |
| GO:0006875 | cellular metal ion homeostasis | 57 | 0.92 | 2.99E-04 |
| GO:0048637 | skeletal muscle development | 61 | 0.92 | 7.96E-11 |
| GO:0006959 | humoral immune response | 52 | 0.92 | 7.46E-04 |
| GO:0007519 | striated muscle development | 103 | 0.91 | 1.19E-10 |
| GO:0055065 | metal ion homeostasis | 58 | 0.91 | 1.99E-04 |
| GO:0030324 | lung development | 59 | 0.89 | 4.07E-04 |
| GO:0007178 | transmembrane receptor protein serine/threonine kinase signaling pathway | 67 | 0.89 | 1.93E-04 |
| GO:0006575 | amino acid derivative metabolic process | 70 | 0.88 | 5.69E-11 |
| GO:0030323 | respiratory tube development | 60 | 0.88 | 4.78E-04 |
| GO:0007229 | integrin-mediated signaling pathway | 74 | 0.88 | 2.91E-04 |
| GO:0048469 | cell maturation | 66 | 0.87 | 4.68E-04 |
| GO:0006817 | phosphate transport | 61 | 0.86 | 2.84E-04 |
| GO:0055074 | calcium ion homeostasis | 53 | 0.86 | 7.58E-04 |
| GO:0045786 | negative regulation of progression through cell cycle | 101 | 0.85 | 5.19E-11 |
| GO:0048732 | gland development | 63 | 0.85 | 6.85E-04 |
| GO:0044271 | nitrogen compound biosynthetic process | 61 | 0.84 | 3.98E-04 |
| GO:0030003 | cellular cation homeostasis | 87 | 0.84 | 1.99E-10 |
| GO:0021700 | developmental maturation | 79 | 0.84 | 2.21E-04 |
| GO:0016311 | dephosphorylation | 105 | 0.83 | 5.97E-10 |
| GO:0055080 | cation homeostasis | 88 | 0.83 | 2.13E-04 |
| GO:0055082 | cellular chemical homeostasis | 90 | 0.82 | 5.43E-11 |
| GO:0006470 | protein amino acid dephosphorylation | 93 | 0.82 | 6.63E-11 |
| GO:0050778 | positive regulation of immune response | 75 | 0.81 | 3.32E-04 |
| GO:0051240 | positive regulation of multicellular organismal process | 94 | 0.81 | 1.76E-04 |
| GO:0008015 | circulation | 84 | 0.81 | 5.43E-04 |
| GO:0050776 | regulation of immune response | 88 | 0.80 | 1.87E-04 |
| GO:0002684 | positive regulation of immune system process | 77 | 0.80 | 4.59E-04 |
| GO:0050801 | ion homeostasis | 103 | 0.79 | 2.99E-10 |
| GO:0002682 | regulation of immune system process | 90 | 0.79 | 2.06E-04 |
| GO:0001503 | ossification | 80 | 0.79 | 4.51E-04 |
| GO:0045165 | cell fate commitment | 94 | 0.78 | 4.42E-04 |
| GO:0015674 | di-, tri-valent inorganic cation transport | 112 | 0.78 | 1.19E-09 |
| GO:0031214 | biomineral formation | 81 | 0.78 | 7.21E-04 |
| GO:0046849 | bone remodeling | 89 | 0.78 | 3.81E-04 |
| GO:0008361 | regulation of cell size | 91 | 0.77 | 4.78E-11 |
| GO:0030005 | cellular di-, tri-valent inorganic cation homeostasis | 81 | 0.77 | 7.08E-04 |
| GO:0043062 | extracellular structure organization and biogenesis | 85 | 0.77 | 6.28E-04 |
| GO:0009968 | negative regulation of signal transduction | 81 | 0.77 | 6.74E-04 |
| GO:0040008 | regulation of growth | 117 | 0.77 | 1.81E-04 |
| GO:0006816 | calcium ion transport | 85 | 0.75 | 8.78E-04 |
| GO:0002009 | morphogenesis of an epithelium | 103 | 0.73 | 4.87E-04 |
| GO:0002252 | immune effector process | 106 | 0.73 | 6.40E-04 |
| GO:0043549 | regulation of kinase activity | 120 | 0.72 | 3.14E-04 |
| GO:0045859 | regulation of protein kinase activity | 115 | 0.72 | 3.73E-04 |
| GO:0051338 | regulation of transferase activity | 121 | 0.72 | 3.06E-04 |
ErmineJ was used to identify significantly overrepresented GO classes in the gastrocnemius as compared with the quadriceps from LFD mice (n = 10). For the concept biological process we selected GO classes with a FDR < 0.001. For this analysis only classes containing 8 through 125 genes were taken into account. N, number of genes in GO class