Table 2.
Microarray results associated with coregulated gene groups.
| Gene List | Representation Factor | P-value | Regulated genes | # in group |
|---|---|---|---|---|
| Up-regulated | ||||
| Mount 8 | 1.9 | <1.6e-14 | 153 | 803 |
| Mount 20 | 1.6 | <0.007 | 27 | 160 |
| Mount 23 | 4.6 | <4.1e-29 | 67 | 143 |
| Mount 24 | 2 | <1.8e-04 | 28 | 133 |
| Mount 27 | 4.8 | <2.9e-20 | 43 | 87 |
| Mount 30 | 1.9 | <0.071 | 7 | 36 |
| Mount 31 | 4.3 | <1.5e-05 | 11 | 25 |
| Amino Acid Metabolism | 1.3 | <0.179 | 14 | 104 |
| Biosynthesis | 1.3 | <0.012 | 65 | 478 |
| Carbohydrate Metabolism | 1.5 | <0.040 | 19 | 121 |
| Cell Structure | 1.4 | <0.042 | 31 | 219 |
| Cell biology | 1.8 | <0.077 | 8 | 44 |
| Collagen | 1.5 | <0.16 | 28 | 179 |
| Energy Generation | 2.1 | <3.0e-04 | 25 | 117 |
| Intestine | 3.6 | <0.041 | 3 | 8 |
| Nucleotide Synthesis | 2.2 | <0.004 | 14 | 62 |
| Proteases | 2.1 | <2.6e-04 | 25 | 116 |
| Protein Expression | 2.2 | <9.9e-14 | 90 | 390 |
| RNA binding | 2.7 | <2.6e-13 | 59 | 209 |
| Down-regulated | ||||
| Mount 7 | 3.1 | <2.3e-28 | 115 | 810 |
| Mount 11 | 3.3 | <1.2e-24 | 90 | 587 |
| DNA Repair Genes | 5.5 | <3.3e-06 | 11 | 44 |
| Germ Line Enriched | 3.6 | <1.2e-24 | 83 | 508 |
| Meiosis | 3.8 | <0.019 | 4 | 23 |
| Mitosis | 2.7 | <0.003 | 10 | 80 |
| Oocyte-enriched | 1.8 | <0.008 | 21 | 258 |
Specific functional groups were found to be over-represented in our 99.0% significant group using Stanford Microarray Database web tools [57]. A representation factor of 1.0 would be expected in a randomly generated list of genes. Higher values show enrichment for genes in that functional group. P values represent the likelihood of achieving that enrichment by chance. Mount 7 contains germline enriched, oocyte, mitosis, and meiosis genes, Mount 8 contains intestinal genes, proteases, carboxylesterases, lipases, and antibacterial proteins. Mount 11 contains germline enriched, oocyte, meiosis, mitosis, retinoblastoma enriched complex. Mount 20 contains germline enriched, biosynthesis, protein expression, and heat shock genes. Mount 23 contains protein expression and energy generation genes. Mount 24 contains amino acid metabolism, lipid metabolism, and fatty acid oxidation genes. Mount 27 contains amino acid metabolism and energy generation genes. Mount 30 contains protein expression genes, and Mount 31 is not characterized. In addition to Mountains, gene expression is also clustered by biofunctional groups. Number of genes in the group represent the number of genes from several experiments that show coregulation of expression for a particular mountain [57].