Table 2.
Hallmark Pathways for DNA Repair, G2M Checkpoint, MYC Targets and E2F Targets Are Up-regulated in MccF/F Mouse Lesions but Down-regulated in Mcc∆IEC Mouse Lesions (shown in bold)
| GSEA hallmark pathway | ES MCCF/F lesions vs normal tissue |
FDR Q value |
ES MCCΔIEC lesions vs normal tissue |
FDR Q value |
ES MCCΔIEC vs MCCF/F lesions vs lesions |
FDR Q value |
|---|---|---|---|---|---|---|
| Inflammation and cancer | ||||||
| Interferon γ response | 0.80 | 0 | 0.78 | 0 | 0.31 | 0.004 |
| Epithelial mesenchymal transition | 0.77 | 0 | 0.78 | 0 | 0.57 | 0 |
| Allograft rejection | 0.76 | 0 | 0.75 | 0 | 0.47 | 0 |
| Interferon α response | 0.80 | 0 | 0.77 | 0 | 0.24 | 0.29 NS |
| Inflammatory response | 0.69 | 0 | 0.74 | 0 | 0.57 | 0 |
| IL6 JAK STAT3 signaling | 0.76 | 0 | 0.78 | 0 | 0.61 | 0 |
| TNFα signaling via NF-κB | 0.68 | 0 | 0.75 | 0 | 0.71 | 0 |
| Angiogenesis | 0.68 | 0 | 0.77 | 0 | 0.53 | 0 |
| TGFβ signaling | 0.57 | 0 | 0.62 | 0 | 0.55 | 0 |
| Apical junction | 0.54 | 0 | 0.61 | 0 | 0.42 | 0 |
| Apical surface | 0.59 | 0 | 0.54 | 6.84E-04 | 0.32 | 0.097 NS |
| Apoptosis | 0.56 | 0 | 0.59 | 0 | 0.46 | 0 |
| KRAS signaling up | 0.55 | 0 | 0.61 | 0 | 0.47 | 0 |
| IL2 STAT5 signaling | 0.55 | 0 | 0.58 | 0 | 0.43 | 0 |
| Hypoxia | 0.51 | 0 | 0.60 | 0 | 0.52 | 0 |
| Complement | 0.62 | 0 | 0.66 | 0 | 0.49 | 0 |
| Coagulation | 0.60 | 0 | 0.66 | 0 | 0.49 | 0 |
| PI3K Akt mTOR signaling | 0.44 | 7.8E-04 | 0.38 | 0.017 | 0.23 | 0.260 NS |
| DNA damage and checkpoints | ||||||
| G2M checkpoint | 0.53 | 0 | -0.30 | 0.093 NS | -0.62 | 0 |
| DNA repair | 0.18 | 0.94 NS | -0.39 | 0.008 | -0.45 | 0 |
| Mitotic spindle | 0.48 | 0 | 0.36 | 0.013 | -0.27 | 0.043 |
| UV response down | 0.47 | 0 | 0.51 | 0 | 0.37 | 4.1E-04 |
| Cell cycling and cell growth | ||||||
| MYC targets v1 | 0.66 | 0 | -0.34 | 0.024 | -0.70 | 0 |
| MYC targets v2 | 0.52 | 1.8E-04 | -0.40 | 0.037 | -0.72 | 0 |
| E2F targets | 0.55 | 0 | -0.48 | 0 | -0.73 | 0 |
| Metabolism | ||||||
| mTORC1 signaling | 0.56 | 0 | 0.39 | 0.004 | -0.34 | 6.0E-04 |
| Unfolded protein response | 0.43 | 9.7E-04 | -0.25 | 0.494 NS | -0.50 | 0 |
| Adipogenesis | -0.37 | 0.004 | -0.45 | 0 | -0.36 | 4.5E-04 |
| Fatty acid metabolism | -0.45 | 0 | -0.52 | 0 | -0.40 | 1.6E-04 |
| Peroxisome | -0.47 | 0 | -0.49 | 0 | -0.29 | 0.075 NS |
| Oxidative phosphorylation | -0.40 | 0.001 | -0.66 | 0 | -0.66 | 0 |
NOTE. Positive ES (maximum, 1) indicates up-regulation of pathway and negative values show down-regulation. Hallmark pathways for G2M checkpoint, DNA repair, MYC targets v1, MYC targets v2 and E2F targets are down-regulated in MccΔIEC lesions compared to MccF/F lesions.
ES, enrichment score; FDR, false discovery rate; IL, interleukin; JAK, Janus kinase; mTOR, Mechanistic Target of Rapamycin Kinase; NF-κB, nuclear factor-κB; PI3K, Phosphoinositide 3-kinase; STAT, Signal Transducers and Activators of Transcription; TGF, transforming growth factor.