TABLE 5.
EASE scores for groups of genes being differentially expressed within the control vs. fast inbreeding comparison and the control vs. slower inbreeding comparison and for genes being differentially expressed with both fast and slower inbreeding
| Contrasts | System | Category | LH | LT | PH | PT | EASE scores |
|---|---|---|---|---|---|---|---|
| Control vs. fast inbreeding | Molecular function | Catalytic activity | 60 | 93 | 2998 | 6508 | 0.0003 |
| Biological process | Regulation of biological process | 6 | 48 | 110 | 4221 | 0.0070 | |
| Cellular component | Lysosyme | 3 | 45 | 17 | 3883 | 0.0153 | |
| Cellular component | Lytic vacuole | 3 | 45 | 17 | 3883 | 0.0153 | |
| Cellular component | Vacuole | 4 | 45 | 51 | 3883 | 0.0194 | |
| Molecular function | Anion transporter activity | 4 | 93 | 41 | 6508 | 0.0198 | |
| Molecular function | Inorganic transporter activity | 3 | 93 | 16 | 6508 | 0.0209 | |
| Molecular function | Mannosidase activity | 3 | 93 | 16 | 6508 | 0.0209 | |
| Biological process | Antibacterial humoral response | 3 | 48 | 22 | 4221 | 0.0243 | |
| Biological process | Response to stress | 7 | 48 | 211 | 4221 | 0.0281 | |
| Molecular function | Transferase activity | 19 | 93 | 804 | 6508 | 0.0307 | |
| Cellular component | Proteasome core complex | 3 | 45 | 25 | 3883 | 0.0319 | |
| Biological process | Carboxylic acid metabolism | 5 | 48 | 121 | 4221 | 0.0444 | |
| Biological process | Organic acid metabolism | 5 | 48 | 121 | 4221 | 0.0444 | |
| Molecular function | Methyltransferase activity | 4 | 93 | 57 | 6508 | 0.0463 | |
| Biological process | Physiological process | 44 | 48 | 3438 | 4221 | 0.0470 | |
| Molecular function | Transferase activity, transferring one-carbon groups | 4 | 93 | 58 | 6508 | 0.0483 | |
| Control vs. slow inbreeding | Biological process | Organic acid metabolism | 13 | 96 | 121 | 4221 | 0.0000 |
| Biological process | Carboxylic acid metabolism | 13 | 96 | 121 | 4221 | 0.0000 | |
| Biological process | Physiological process | 92 | 96 | 3438 | 4221 | 0.0000 | |
| Biological process | Metabolism | 72 | 96 | 2302 | 4221 | 0.0000 | |
| Molecular function | Catalytic activity | 114 | 190 | 2998 | 6508 | 0.0001 | |
| Molecular function | Oxidoreductase activity | 26 | 190 | 421 | 6508 | 0.0002 | |
| Biological process | Pyruvate metabolism | 4 | 96 | 10 | 4221 | 0.0012 | |
| Molecular function | Transaminase activity | 5 | 190 | 17 | 6508 | 0.0012 | |
| Molecular function | Transferase activity, transferring nitrogenous groups | 5 | 190 | 17 | 6508 | 0.0012 | |
| Biological process | Ubiquitin-dependent protein catabolism | 5 | 96 | 22 | 4221 | 0.0013 | |
| Biological process | Antibacterial humoral response | 5 | 96 | 22 | 4221 | 0.0013 | |
| Biological process | Modification-dependent protein catabolism | 5 | 96 | 24 | 4221 | 0.0018 | |
| Biological process | Amino acid metabolism | 8 | 96 | 79 | 4221 | 0.0018 | |
| Cellular component | Cytoplasm | 59 | 104 | 1642 | 3883 | 0.0026 | |
| Cellular component | Mitochondrial matrix | 11 | 104 | 145 | 3883 | 0.0046 | |
| Molecular function | Cyclohydrolase activity | 3 | 190 | 4 | 6508 | 0.0048 | |
| Molecular function | Glycine hydroxymethyltransferase activity | 3 | 190 | 4 | 6508 | 0.0048 | |
| Biological process | ATP-dependent proteolysis | 4 | 96 | 17 | 4221 | 0.0060 | |
| Biological process | Defense response to bacteria | 5 | 96 | 36 | 4221 | 0.0082 | |
| Molecular function | Ligase activity, forming carbon nitrogen bonds | 7 | 190 | 63 | 6508 | 0.0095 | |
| Biological process | Amino acid and derivative metabolism | 8 | 96 | 107 | 4221 | 0.0098 | |
| Molecular function | Inositol-1(or 4)-monophosphatase activity | 3 | 190 | 6 | 6508 | 0.0117 | |
| Cellular component | Intracellular | 84 | 104 | 2732 | 3883 | 0.0119 | |
| Biological process | Lipid metabolism | 6 | 96 | 63 | 4221 | 0.0130 | |
| Biological process | Amine metabolism | 8 | 96 | 113 | 4221 | 0.0130 | |
| Molecular function | Oxidoreductase activity, acting on CH-OH group of donors | 9 | 190 | 110 | 6508 | 0.0143 | |
| Biological process | Response to bacteria | 5 | 96 | 43 | 4221 | 0.0152 | |
| Biological process | Serine family amino acid metabolism | 3 | 96 | 9 | 4221 | 0.0163 | |
| Biological process | Nucleotide metabolism | 4 | 96 | 25 | 4221 | 0.0177 | |
| Molecular function | Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 7 | 190 | 77 | 6508 | 0.0239 | |
| Molecular function | Methyltransferase activity | 6 | 190 | 57 | 6508 | 0.0242 | |
| Molecular function | Lyase activity | 9 | 190 | 122 | 6508 | 0.0252 | |
| Molecular function | Transferase activity, transferring one-carbon groups | 6 | 190 | 58 | 6508 | 0.0259 | |
| Cellular component | Mitochondrion | 21 | 104 | 484 | 3883 | 0.0270 | |
| Cellular component | Proteasome core complex | 4 | 104 | 25 | 3883 | 0.0273 | |
| Molecular function | Oxidoreductase activity, acting on the aldehyde or oxo group of donors | 4 | 190 | 23 | 6508 | 0.0278 | |
| Molecular function | Hydrolyase activity | 5 | 190 | 40 | 6508 | 0.0279 | |
| Molecular function | Structural constituent of cytoskeleton | 5 | 190 | 42 | 6508 | 0.0327 | |
| Molecular function | Chaperone activity | 7 | 190 | 87 | 6508 | 0.0402 | |
| Cellular component | Proteasome complex | 5 | 104 | 50 | 3883 | 0.0423 | |
| Biological process | Antimicrobial humoral response | 5 | 96 | 60 | 4221 | 0.0450 | |
| Molecular function | Oxidoreductase activity, acting on the CH-NH2 group of donors | 3 | 190 | 12 | 6508 | 0.0457 | |
| Biological process | Response to stress | 10 | 96 | 211 | 4221 | 0.0464 | |
| Molecular function | Carbon-oxygen lyase activity | 5 | 190 | 48 | 6508 | 0.0497 | |
| Control vs. inbreeding | Molecular function | Methyltransferase activity | 4 | 35 | 57 | 6508 | 0.0031 |
| Molecular function | Catalytic activity | 25 | 35 | 2998 | 6508 | 0.0033 | |
| Molecular function | Transferase activity, transferring one-carbon groups | 4 | 35 | 58 | 6508 | 0.0033 | |
| Biological process | Regulation of biological process | 4 | 21 | 110 | 4221 | 0.0142 | |
| Biological process | Carboxylic acid metabolism | 4 | 21 | 121 | 4221 | 0.0183 | |
| Biological process | Organic acid metabolism | 4 | 21 | 121 | 4221 | 0.0183 | |
| Biological process | Organismal physiological process | 6 | 21 | 411 | 4221 | 0.0387 |
The genes were grouped by “system” (molecular function, biological process, or cellular component) and “category” within the systems by the EASE application on the DAVID homepage (http://david.niaid.nih.gov/david/ease.htm). Categories with significant EASE scores (<0.05) are presented here. LH represents number of genes in gene list assigned to category; LT represents number of genes in gene list assigned to system; PH represents the number of all known genes assigned to category; and PT represents the number of all known genes in that system. The representation of each category of genes (only categories represented by at least three genes are included) was evaluated by the EASE-score criteria. The test calculates the probability of detecting the actual detected number of genes in a category, by evaluating the proportion of genes in each gene list belonging to a category vs. the proportion of genes belonging to this category out of all known genes. Thus, the ratio LH/LT is compared to the ratio PH/PT.