Table 1.
Sample-specific master regulators predicted from sample-specific gene signatures
| Cell line | Cancer type | Number of master TFs/motifs | Master TFsa | Number of cancer-type relevant or driver genes associated with master TFs |
|---|---|---|---|---|
| HCT-116 | Colon | 3/42 | ATF3, DDIT3, NFE2L2 | 347 |
| HT-29 | Colon | 15/254 | ETS2, FGF19, GPD1, HDAC1, HNF1A, KLF4, KLF5, KLF6, MZF1, NR1H3, PPARG, RELA, RXRA, SP1, ZBTB7A | 448 |
| MDA-MB-231 | Breast | 4/111 | ETS1, ETV1, FOSL1, STAT5A | 419 |
| SK-MEL-5 | Melanoma | 20/211 | BAX, CAT, CTCFL, CTNNB1, E2F3, ETV4, HHAT, MITF, MXI1, NR4A1, OLIG2, PAX3, PIR, PPARGC1A, RAB7A, RUNX3, SNAI2, SOX10, TBX2, TFAP2A | 263 |
| DU-145 | Prostate | 4/99 | FOSL1, HOXA1, SETDB1, YY1 | 345 |
| SKOV-3 | Ovarian | 1/31 | ZEB1 | 284 |
| OVCAR-3 | Ovarian | 2/62 | EGR1, FOS | 255 |
| A549 | Lung | 3/67 | CEBPB, NFE2L2, TP63 | 304 |
| COLO-205 | Colon | 7/160 | BCLAF1, CLOCK, ELF3, HNF1A, HOXB13, PITX1, TFF3 | 445 |
| PC-3 | Prostate | 7/216 | ELK1, ETV1, ETV4, FOSL1, HOXB13, MTHFD1, SPDEF | 427 |
The table lists the number of predicted master regulators per cell line (together with the number of motifs directly associated with these transcription factors (TFs); the names of the master TFs (bold indicating gains), and finally the number of candidate over-expressed cancer type-related or driver genes (near these genes we score mutations for motif gains)