Table 3.
GSEA on the Intersect 2 genes from Figure 4C against the MSigDB hallmark gene sets.
| INTERSECT 2 GSEA | ||||||
|---|---|---|---|---|---|---|
| Gene set name | # Genes in gene set (K) | Description | # Genes in overlap (k) | k/K | p-value | FDR (q-value) |
| HALLMARK_INTERFERON_ GAMMA_RESPONSE |
200 | Genes up-regulated in response to IFNG [GeneID = 3458]. | 60 | 0.3 | 3.53E-38 | 1.76E-36 |
| HALLMARK_INTERFERON_ ALPHA_RESPONSE |
97 | Genes up-regulated in response to alpha interferon proteins. | 43 | 0.4433 | 4.26E-36 | 1.06E-34 |
| HALLMARK_HYPOXIA | 200 | Genes up-regulated in response to low oxygen levels (hypoxia). | 39 | 0.195 | 5.11E-18 | 8.51E-17 |
| HALLMARK_P53_PATHWAY | 200 | Genes involved in p53 pathways and networks. | 33 | 0.165 | 2.66E-13 | 3.33E-12 |
| HALLMARK_APOPTOSIS | 161 | Genes mediating programmed cell death (apoptosis) by activation of caspases. | 28 | 0.1739 | 4.49E-12 | 4.49E-11 |
| HALLMARK_ESTROGEN_RESPONSE_ EARLY |
200 | Genes defining early response to estrogen. | 31 | 0.155 | 7.51E-12 | 4.70E-11 |
| HALLMARK_HEME_METABOLISM | 200 | Genes involved in metabolism of heme (a cofactor consisting of iron and porphyrin) and erythroblast differentiation. | 31 | 0.155 | 7.51E-12 | 4.70E-11 |
| HALLMARK_MYOGENESIS | 200 | Genes involved in development of skeletal muscle (myogenesis). | 31 | 0.155 | 7.51E-12 | 4.70E-11 |
| HALLMARK_PROTEIN_SECRETION | 96 | Genes involved in protein secretion pathway. | 21 | 0.2188 | 2.31E-11 | 1.28E-10 |
| HALLMARK_EPITHELIAL_ MESENCHYMAL_TRANSITION |
200 | Genes defining epithelial-mesenchymal transition, as in wound healing, fibrosis and metastasis. | 30 | 0.15 | 3.77E-11 | 1.89E-10 |
| HALLMARK_ESTROGEN_RESPONSE_ LATE |
200 | Genes defining late response to estrogen. | 29 | 0.145 | 1.82E-10 | 8.29E-10 |
| HALLMARK_APICAL_JUNCTION | 200 | Genes encoding components of apical junction complex. | 28 | 0.14 | 8.47E-10 | 3.53E-09 |
| HALLMARK_IL2_STAT5_ SIGNALING |
200 | Genes up-regulated by STAT5 in response to IL2 stimulation. | 26 | 0.13 | 1.62E-08 | 5.77E-08 |
| HALLMARK_KRAS_SIGNALING_DN | 200 | Genes down-regulated by KRAS activation. | 26 | 0.13 | 1.62E-08 | 5.77E-08 |
| HALLMARK_ALLOGRAFT_REJECTION | 200 | Genes up-regulated during transplant rejection. | 25 | 0.125 | 6.63E-08 | 2.21E-07 |
| HALLMARK_UNFOLDED_ PROTEIN_RESPONSE |
113 | Genes up-regulated during unfolded protein response, a cellular stress response related to the endoplasmic reticulum. | 18 | 0.1593 | 1.16E-07 | 3.62E-07 |
| HALLMARK_ADIPOGENESIS | 200 | Genes up-regulated during adipocyte differentiation (adipogenesis). | 24 | 0.12 | 2.60E-07 | 6.83E-07 |
| HALLMARK_TNFA_SIGNALING_ VIA_NFKB |
200 | Genes regulated by NF-kB in response to TNF [GeneID = 7124]. | 24 | 0.12 | 2.60E-07 | 6.83E-07 |
| HALLMARK_XENOBIOTIC_ METABOLISM |
200 | Genes encoding proteins involved in processing of drugs and other xenobiotics. | 24 | 0.12 | 2.60E-07 | 6.83E-07 |
| HALLMARK_IL6_JAK_ STAT3_SIGNALING |
87 | Genes up-regulated by IL6 [GeneID = 3569] via STAT3 [GeneID = 6774], e.g., during acute phase response. | 15 | 0.1724 | 4.51E-07 | 1.13E-06 |