Table 6.
Enriched KEGG pathways for the list of CD4 T-cell NOD altered genes.
| KEGG pathway | Adjusted p-value | No. of genes | Genes in the pathway |
|---|---|---|---|
| 2 wk | |||
| Metabolic pathways | 1.01e-5 | 9 | Enpp3, Ndufs5, Galnt10, Prim2, Gatm, Dnmt3b, Akr1e1, Enpp1, Rrm1 |
| Purine metabolism | 5.22e-5 | 4 | Enpp3, Prim2, Enpp1, Rrm1 |
| Pantothenate and CoA biosynthesis | 0.0001 | 2 | Enpp3, Enpp1 |
| Riboflavin metabolism | 0.0001 | 2 | Enpp3, Enpp1 |
| Nicotinate and nicotinamide metabolism | 0.0003 | 2 | Enpp3, Enpp1 |
| Starch and sucrose metabolism | 0.0008 | 2 | Enpp3, Enpp1 |
| Pyrimidine metabolism | 0.0039 | 2 | Prim2, Rrm1 |
| 3 wk | |||
| Metabolic pathways | 0.0005 | 10 | Enpp3, Ndufs5, Galnt10, Prim2, Gatm, Inppl1, Dnmt3b, Akr1e1, Dut, Enpp1 |
| Riboflavin metabolism | 0.0008 | 2 | Enpp3, Enpp1 |
| Purine metabolism | 0.0008 | 4 | Enpp3, Prim2, Enpp1 |
| Pantothenate and CoA biosynthesis | 0.0008 | 2 | Enpp3, Enpp1 |
| Pyrimidine metabolism | 0.0013 | 3 | Prim2, Pnpt1, Dut |
| Nicotinate and nicotinamide metabolism | 0.0008 | 2 | Enpp3, Enpp1 |
| Spliceosome | 0.0029 | 3 | Crnkl1, Srnp200, Snw1 |
| Starch and sucrose metabolism | 0.0031 | 2 | Enpp3, Enpp1 |
| 4 wk | |||
| Metabolic pathways | 0.0002 | 7 | Enpp3, Ndufs5, Galnt10, Prim2, Gatm, Pigv, Mdh1 |
| Pyruvate metabolism | 0.0008 | 2 | Acyp2, Mdh1 |
One-way ANOVA (p < 0.005, Benjamini–Hochberg) of mRNA expression data followed by hierarchical clustering identified 58, 115, and 65 probe sets 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). The lists of differentially expressed genes were analyzed in WebGestalt (http://bioinfo.vanderbilt.edu/webgestalt) for enriched KEGG pathways using the hypergeometric test (p < 0.01, Benjamini–Hochberg). Pathways represented by =2 genes are shown. Pathways or genes indicated in bold font were common to the 3 age groups.