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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)