Table 2.
Top Hallmark Gene Sets Differentially Expressed in the Stroma Between EMT-High (PAC010) and EMT-Low (PAC006) Identified by GSEA. A: Top 10 positively enriched gene sets. B: Top 10 gene sets that were negatively enriched. NES, normalized enrichment score; FDR, false discovery rate. Size is the number of genes of the pathway.
| A | Gene Set (Positively Enriched) | Size | NES | FDR q-Val |
|---|---|---|---|---|
| 1 | TNFA signaling via NFKB | 180 | 2.14 | 0.000 |
| 2 | E2F targets | 195 | 2.14 | 0.000 |
| 3 | G2M checkpoint | 188 | 2.09 | 0.000 |
| 4 | Inflammatory response | 163 | 1.93 | 0.000 |
| 5 | IL6 JAK STAT3 signaling | 73 | 1.92 | 0.000 |
| 6 | Interferon alpha response | 86 | 1.91 | 0.000 |
| 7 | Unfolded protein response | 107 | 1.90 | 0.000 |
| 8 | MTORC1 signaling | 197 | 1.84 | 0.000 |
| 9 | Hypoxia | 159 | 1.81 | 0.001 |
| 10 | Glycolysis | 166 | 1.79 | 0.001 |
| B | Gene Set (Negatively Enriched) | Size | NES | FDR q-Val |
| 1 | Adipogenesis | 174 | −2.22 | 0.000 |
| 2 | Myogenesis | 122 | −2.20 | 0.000 |
| 3 | Bile acid metabolism | 74 | −1.98 | 0.000 |
| 4 | Oxidative phosphorylation | 185 | −1.92 | 0.000 |
| 5 | Hedgehog signaling | 28 | −1.84 | 0.002 |
| 6 | Estrogen response early | 151 | −1.61 | 0.021 |
| 7 | KRAS signaling DN | 80 | −1.61 | 0.018 |
| 8 | Fatty acid metabolism | 128 | −1.59 | 0.017 |
| 9 | Notch signaling | 27 | −1.59 | 0.017 |
| 10 | Estrogen response late | 147 | −1.53 | 0.025 |