Table 2. Selected GO categories over-represented among genes predicted to be under positive selection.
| Gene number | Fold | P-value | P-value | ||||
| Category | Description | All | PSGs | E[PSGs] | Enrich. | MWU | FET |
| Biological process | |||||||
| GO:0007606 | sensory perception of chemical stimulus | 255 | 24 | 6.2 | 3.9 | 4.3×10−39 | 1.5×10−08 |
| GO:0007608 | sensory perception of smell | 229 | 15 | 5.5 | 2.7 | 6.1×10−31 | 4.8×10−04 |
| GO:0002526 | acute inflammatory response | 55 | 11 | 1.3 | 8.3 | 4.7×10−11 | 6.7×10−08 |
| GO:0050909 | sensory perception of taste | 25 | 8 | 0.6 | 13.2 | 1.4×10−10 | 8.3×10−08 |
| GO:0009611 | response to wounding | 321 | 23 | 7.8 | 3.0 | 3.2×10−10 | 6.9×10−06 |
| GO:0002541 | activation of plasma proteins during acute inflammatory response | 28 | 7 | 0.7 | 10.3 | 1.3×10−09 | 3.5×10−06 |
| GO:0006956 | complement activation | 28 | 7 | 0.7 | 10.3 | 1.3×10−09 | 3.5×10−06 |
| GO:0045087 | innate immune response | 70 | 8 | 1.7 | 4.7 | 1.9×10−09 | 3.7×10−04 |
| GO:0009615 | response to virus | 69 | 7 | 1.7 | 4.2 | 3.0×10−08 | 2.4×10−03 |
| GO:0009617 | response to bacterium | 67 | 6 | 1.6 | 3.7 | 4.2×10−08 | 7.9×10−03 |
| GO:0002682 | regulation of immune system process | 60 | 11 | 1.5 | 7.6 | 8.5×10−08 | 1.0×10−06 |
| GO:0016064 | immunoglobulin mediated immune response | 36 | 8 | 0.9 | 9.2 | 1.1×10−07 | 1.5×10−05 |
| GO:0007186 | G-protein coupled receptor protein signaling pathway | 792 | 39 | 19.2 | 2.0 | 1.4×10−07 | 2.5×10−05 |
| GO:0006959 | humoral immune response | 56 | 9 | 1.4 | 6.6 | 1.6×10−07 | 7.2×10−06 |
| GO:0050778 | positive regulation of immune response | 49 | 9 | 1.2 | 7.6 | 1.7×10−07 | 8.4×10−06 |
| GO:0002455 | humoral immune response mediated by circulating immunoglobulin | 24 | 6 | 0.6 | 10.3 | 3.0×10−07 | 1.8×10−05 |
| GO:0019724 | B cell mediated immunity | 37 | 8 | 0.9 | 8.9 | 3.2×10−07 | 1.8×10−05 |
| GO:0006968 | cellular defense response | 55 | 5 | 1.3 | 3.8 | 3.5×10−07 | 1.1×10−02 |
| GO:0019882 | antigen processing and presentation | 27 | 4 | 0.7 | 6.1 | 5.7×10−07 | 5.0×10−03 |
| GO:0006958 | complement activation, classical pathway | 23 | 6 | 0.6 | 10.8 | 6.1×10−07 | 1.4×10−05 |
| GO:0050877 | neurological process | 811 | 34 | 19.6 | 1.7 | 7.5×10−07 | 1.5×10−03 |
| GO:0006957 | complement activation, alternative pathway | 11 | 2 | 0.3 | 7.5 | 1.5×10−06 | 2.8×10−02 |
| GO:0019835 | cytolysis | 15 | 3 | 0.4 | 8.3 | 2.2×10−06 | 5.2×10−03 |
| GO:0002449 | lymphocyte mediated immunity | 53 | 10 | 1.3 | 7.8 | 5.7×10−06 | 2.5×10−06 |
| GO:0002460 | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 57 | 13 | 1.4 | 9.4 | 8.0×10−06 | 1.1×10−08 |
| GO:0002250 | adaptive immune response | 58 | 13 | 1.4 | 9.3 | 1.5×10−05 | 1.1×10−08 |
| GO:0007338 | single fertilization | 39 | 4 | 0.9 | 4.2 | 1.7×10−05 | 1.4×10−02 |
| Molecular function | |||||||
| GO:0004984 | olfactory receptor activity | 229 | 15 | 5.5 | 2.7 | 6.9×10−36 | 6.8×10−04 |
| GO:0004930 | G-protein coupled receptor activity | 625 | 37 | 15.1 | 2.4 | 2.5×10−14 | 5.1×10−07 |
| GO:0004888 | (*) transmembrane receptor activity | 972 | 55 | 23.5 | 2.3 | 4.0×10−12 | 3.3×10−09 |
| GO:0008527 | taste receptor activity | 14 | 5 | 0.3 | 14.8 | 1.3×10−08 | 1.4×10−05 |
| GO:0008009 | chemokine activity | 34 | 5 | 0.8 | 6.1 | 3.7×10−07 | 1.3×10−03 |
| GO:0004866 | endopeptidase inhibitor activity | 110 | 6 | 2.7 | 2.3 | 4.1×10−07 | 5.1×10−02 |
| GO:0019965 | interleukin binding | 33 | 1 | 0.8 | 1.3 | 2.2×10−06 | 5.5×10−01 |
| GO:0005125 | cytokine activity | 184 | 13 | 4.5 | 2.9 | 7.8×10−06 | 5.8×10−04 |
| GO:0008173 | RNA methyltransferase activity | 19 | 1 | 0.5 | 2.2 | 8.4×10−06 | 3.7×10−01 |
| GO:0004907 | interleukin receptor activity | 28 | 1 | 0.7 | 1.5 | 1.1×10−05 | 5.0×10−01 |
| GO:0017171 | serine hydrolase activity | 150 | 9 | 3.6 | 2.5 | 2.1×10−05 | 1.1×10−02 |
| Cellular component | |||||||
| GO:0005615 | extracellular space | 354 | 19 | 8.6 | 2.2 | 6.8×10−08 | 4.1×10−03 |
| GO:0042611 | MHC protein complex | 14 | 4 | 0.3 | 11.8 | 2.8×10−07 | 2.8×10−04 |
| GO:0016021 | (*) integral to membrane | 3799 | 168 | 91.9 | 1.8 | 8.9×10−06 | 1.0×10−16 |
Shown are numbers of PSGs and of all genes (out of 16,529 considered) assigned to each category or a descendant category, and one-sided (nominal) P-values from the Mann-Whitney U (MWU) and Fisher's exact (FET) tests (see Methods). Only the 400 PSGs from the test for selection on any branch of the phylogeny are considered here. Note that the MWU P -values do not consider whether or not each gene is predicted to be a PSG, but instead indicate the degree to which the LRT P -values for the genes of each category are shifted toward small values. Consequently, classes of genes experiencing relaxation of constraint but not positive selection may obtain small MWU P -values. In contrast, the FET P -values indicate over-representation of the identified PSGs within each category (or, equivalently, over-representation of each category among the PSGs). Bold indicates significance after a conservative correction for multiple testing (FWER<0.05, Holm correction). The two categories with asterisks are enriched for long genes (see Text S1). Only selected categories FWER-significant P -values under the MWU test are shown; see Table S2 for a complete list.