Table 2.
Representative signaling pathways over-represented in IPA or with enhanced up- or down-regulated gene sets in GSEA in any one of the genotypes in response to 1 Gy IR. Coding represents a single pathway or may represent an average of -log10 (p-values) or FDR q-values of more than 1 related pathway or gene set, such as KEGG and Biocarta p53 signaling pathways. These are not meant to indicate statistical significance but rather relationships. Coded values in the table are italicized and bold to focus on differences between genotypes. As a reference, negative log10 (p-value) and FDR q-value cutoffs considered statistically significant in this work are bolded.
| Cell line | Program | NFKB Signaling | CD40 Signaling | ATM Signaling | p53 Signaling (includes intrinsic apoptosis) | PI3K-ERBB; PIP3-AKT Signaling | G protein; Adenylate cyclase Signaling | RHO GTPase Signaling – down regulated genes | Cell cycle: G2/M checkpoint and mitotic progression – down regulated genes |
|---|---|---|---|---|---|---|---|---|---|
| WT | IPA | 4 | 4 | 3 | 4 | - | - | - | - |
| GSEA | 3 | 4 | 4 | 4 | 2 | 0 | 2 | 2 | |
| H2ax-/- | IPA | 4 | 4 | 4 | 4 | - | - | - | - |
| GSEA | 4 | 4 | 4 | 4 | 0 | 0 | 3 | 2 | |
| 53bp1-/- | IPA | 4 | 4 | 2 | 4 | - | - | - | - |
| GSEA | 3 | 3 | 4 | 4 | 2 | 0 | 4 | 3 | |
| Scid | IPA | 3 | 4 | 2 | 4 | - | - | - | - |
| GSEA | 4 | 4 | 4 | 4 | 3 | 0 | 1 | 4 | |
| Mdc1-/- | IPA | 3 | 4 | 2 | 4 | - | - | - | - |
| GSEA | 4 | 4 | 4 | 4 | 4 | 0 | 1 | 3 | |
| Mre11A/A | IPA | 2 | 2 | 2 | 4 | - | - | - | - |
| GSEA | 0 | 1 | 4 | 4 | 2 | 0 | 0 | 0 | |
| Atm-/- | IPA | 0 | 0 | 0 | 0 | - | - | - | - |
| GSEA | 0 | 0 | 0 | 0 | 0 | 4 | 1 | 1 | |
| Ingenuity Canonical Pathways | Gene Set Enrichment Analysis | ||||||||
| Table code | -log10 (p-value) | equivalent p-value | Table code | FDR q-value | |||||
| 4 | ≥ 3.3 | ≤ 0.0005 | 4 | ≤ 0.10 | |||||
| 3 | ≥ 2.3 | ≤ 0.005 | 3 | ≤ 0.25 | |||||
| 2 | ≥ 1.3 | ≤ 0.05 | 2 | ≤ 0.50 | |||||
| 1 | > 0 | ≤ 0.00 | 1 | ≤ 0.75 | |||||
| 0 | 0 | 0 | 0 | > 0.75 | |||||