TABLE 1.
Gene Ontology analysis of genes that changed ≥2-fold significantly (FDR-corrected p < 0.05) upon 24 h of Sindbis-GFP treatment compared to control.
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Pathways, Molecular Function and Biological Process identifiers that are enriched in the set of genes that are regulated by 24h of Sindbis transduction |
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| ID | Term | Annotated | Regulated | Expected | Fold Enrichment | Raw P-value | FDR |
| Pathways | |||||||
| P00031 | Inflammation mediated by chemokine and cytokine signaling pathway | 187 | 39 | 14.49 | 2.69 | 3.11E-07 | 2.52E-05 |
| P00006 | Apoptosis signaling pathway | 80 | 21 | 6.2 | 3.39 | 8.24E-06 | 4.45E-04 |
| P00054 | Toll receptor signaling pathway | 39 | 13 | 3.02 | 4.3 | 5.82E-05 | 2.36E-03 |
| Molecular function | |||||||
| GO:0003824 | Catalytic activity | 3107 | 331 | 240.82 | 1.37 | 1.70E-09 | 3.14E-07 |
| GO:0005515 | Protein binding | 1855 | 199 | 143.78 | 1.38 | 6.86E-06 | 2.54E-04 |
| GO:0005125 | Cytokine activity | 106 | 25 | 8.22 | 3.04 | 5.98E-06 | 2.77E-04 |
| GO:0016491 | Oxidoreductase activity | 462 | 67 | 35.81 | 1.87 | 4.83E-06 | 2.98E-04 |
| GO:0016787 | Hydrolase activity | 1350 | 152 | 104.64 | 1.45 | 9.88E-06 | 3.05E-04 |
| GO:0008009 | Chemokine activity | 24 | 10 | 1.86 | 5.38 | 9.48E-05 | 2.51E-03 |
| GO:0005102 | Receptor binding | 625 | 78 | 48.44 | 1.61 | 1.27E-04 | 2.95E-03 |
| GO:0008233 | Peptidase activity | 306 | 44 | 23.72 | 1.86 | 3.20E-04 | 6.58E-03 |
| GO:0005488 | Binding | 3686 | 337 | 285.7 | 1.18 | 8.97E-04 | 1.38E-02 |
| GO:0005126 | Cytokine receptor binding | 55 | 13 | 4.26 | 3.05 | 9.83E-04 | 1.40E-02 |
| GO:0005243 | Gap junction channel activity | 19 | 7 | 1.47 | 4.75 | 1.91E-03 | 2.53E-02 |
| Biological process | |||||||
| GO:0002376 | Immune system process | 525 | 88 | 40.69 | 2.16 | 4.02E-10 | 1.40E-08 |
| GO:0034341 | Response to interferon-gamma | 44 | 20 | 3.41 | 5.86 | 1.08E-08 | 3.29E-07 |
| GO:0065009 | Regulation of molecular function | 313 | 55 | 24.26 | 2.27 | 1.97E-07 | 5.33E-06 |
| GO:0050790 | Regulation of catalytic activity | 263 | 46 | 20.38 | 2.26 | 3.22E-06 | 6.52E-05 |
| GO:0019221 | Cytokine-mediated signaling pathway | 40 | 15 | 3.1 | 4.84 | 5.02E-06 | 9.38E-05 |
| GO:0016032 | Viral process | 11 | 7 | 0.85 | 8.21 | 1.54E-04 | 2.67E-03 |
| GO:0000165 | MAPK cascade | 240 | 37 | 18.6 | 1.99 | 2.38E-04 | 3.61E-03 |
| GO:0006520 | Cellular amino acid metabolic process | 186 | 31 | 14.42 | 2.15 | 2.68E-04 | 3.84E-03 |
| GO:0040011 | Locomotion | 248 | 37 | 19.22 | 1.92 | 4.49E-04 | 5.74E-03 |
| GO:0006950 | Response to stress | 488 | 60 | 37.82 | 1.59 | 9.97E-04 | 1.15E-02 |
| GO:0032502 | Developmental process | 1063 | 114 | 82.39 | 1.38 | 9.94E-04 | 1.21E-02 |
| GO:0006629 | Lipid metabolic process | 361 | 47 | 27.98 | 1.68 | 1.27E-03 | 1.41E-02 |
| GO:0009063 | Cellular amino acid catabolic process | 50 | 12 | 3.88 | 3.1 | 1.36E-03 | 1.44E-02 |
| GO:0019220 | Regulation of phosphate metabolic process | 351 | 46 | 27.21 | 1.69 | 1.50E-03 | 1.52E-02 |
| GO:0006955 | Immune response | 296 | 39 | 22.94 | 1.7 | 2.65E-03 | 2.47E-02 |
| GO:0006968 | Cellular defense response | 84 | 16 | 6.51 | 2.46 | 2.56E-03 | 2.49E-02 |
| GO:0006928 | Cellular component movement | 350 | 44 | 27.13 | 1.62 | 3.93E-03 | 3.41E-02 |
| GO:0009605 | Response to external stimulus | 300 | 39 | 23.25 | 1.68 | 3.83E-03 | 3.44E-02 |
| GO:0030097 | Hemopoiesis | 11 | 5 | 0.85 | 5.86 | 4.27E-03 | 3.58E-02 |
| GO:0007399 | Nervous system development | 218 | 30 | 16.9 | 1.78 | 5.87E-03 | 4.60E-02 |
| GO:0006796 | Phosphate-containing compound metabolic process | 1084 | 110 | 84.02 | 1.31 | 6.15E-03 | 4.67E-02 |
Fisher’s exact test with FDR correction was performed. Annotated = number of genes on the array with a specific identifier. Regulated = number of genes in the list of regulated genes with a specific identifier. Expected = number of genes with a specific identifier that is expected to occur in the list of regulated genes, if the regulated genes were a random subset of the annotated genes.