Table 5.
Enriched Gene ontology categories for the list of CD4 T-cell NOD altered genes.
| GO category | 2 wk (134 genes) |
3 wk (252 genes) |
4 wk (185 genes) |
|||
|---|---|---|---|---|---|---|
| No. of genes in category | p-value | No. of genes in category | p-value | No. of genes in category | p-value | |
| Biological process | ||||||
| Cellular metabolism | 53 | 4.24e-5 | 88 | 1.13e-3 | 67 | 1.88e-3 |
| Primary metabolism | 52 | 2.82e-5 | 86 | 7.06e-4 | - | - |
| Nucleobase, nucleoside, nucleotide and nucleic acid metabolism | 28 | 2.02e-3 | - | - | 35 | 8.88e-3 |
| Biopolymer modification | - | - | 25 | 6.53e-3 | - | - |
| Localization | - | - | 43 | 1.13e-3 | - | - |
| Cytoskeletal organization and biogenesis | - | - | 11 | 9.07e-3 | - | - |
| Transport | - | - | 36 | 7.49e-3 | - | - |
| Intracellular transport | - | - | 16 | 1.64e-3 | - | - |
| Secretion | - | - | 8 | 5.70e-3 | - | - |
| Leukocyte activation | - | - | 6 | 8.80e-3 | - | - |
| T cell activation | - | - | 5 | 3.17e-3 | - | - |
| Regulation of hydrolase activity | - | - | 4 | 8.07e-3 | - | - |
| Molecular function | ||||||
| Catalytic activity | - | - | - | - | 60 | 2.89e-3 |
| Hydrolase activity | 22 | 2.84e-3 | 40 | 7.88e-4 | 30 | 2.30e-3 |
| Hydrolase activity, acting on ester bonds | 10 | 3.01e-3 | 15 | 6.23e-3 | 14 | 8.65e-4 |
| Phosphoric ester hydrolase activity | 7 | 1.32e-3 | 10 | 1.99e-3 | 10 | 1.75e-4 |
| Hydrolase activity, acting on acid anhydrides | - | - | 16 | 4.48e-4 | - | - |
| Pyrophosphatase activity | - | - | 15 | 1.12e-3 | - | - |
| GTPase activity | - | - | 6 | 3.49e-3 | - | - |
| Nucleotidyltransferase activity | - | - | 5 | 7.76e-3 | 6 | 2.82e-4 |
| Inositol or phosphatidylinositol phosphatase activity | - | - | - | - | 4 | 1.63e-4 |
| Binding | - | - | 140 | 3.87e-5 | 99 | 4.64e-3 |
| Metal ion binding | - | - | 55 | 2.85e-3 | 43 | 2.02e-3 |
| Protein binding | - | - | 69 | 1.89e-3 | ||
| Cation binding | 28 | 8.09e-3 | 39 | 6.74e-3 | ||
| Transition metal ion binding | 26 | 2.49e-3 | 34 | 4.44e-4 | ||
| Zinc ion binding | 24 | 6.04e-5 | 29 | 5.59e-4 | ||
| Nucleic acid binding | 28 | 4.70e-3 | ||||
| Cellular component | ||||||
| Intracellular | 65 | 2.81e-5 | 113 | 2.35e-7 | 79 | 5.64e-4 |
| Intracellular organelle | 53 | 1.22e-3 | 88 | 9.33e-4 | - | - |
| Intracellular membrane-bound organelle | 48 | 1.39e-3 | 80 | 6.71e-4 | - | - |
| Nucleus | 33 | 8.06e-3 | - | - | - | - |
| Cytoplasm | - | - | 58 | 1.38e-4 | - | - |
| Endoplasmic reticulum | - | - | 15 | 1.72e-3 | - | - |
One-way ANOVA (p < 0.05, Benjamini–Hochberg) of mRNA expression data followed by hierarchical clustering identified 134, 252, and 185 different genes at 2, 3, and 4 weeks, respectively, whose expression was altered in CD4 T-cells from NOD mice compared to two control strains (NOR and C57BL/6). These lists of NOD altered genes were analyzed in WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt) using the hypergeometric test (p < 0.01). Categories represented by = 4 genes are shown. Dashes indicate that the corresponding categories were not significantly enriched at the respective ages. Categories indicated in bold font were common to all 3 age groups.