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Table 1 Sample-specific master regulators predicted from sample-specific gene signatures

From: Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks

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
  1. 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)
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