Table 1 Detection of transcriptional cooperation by multi-omics integration of complementary data and analysis techniques

From: A network of epigenomic and transcriptional cooperation encompassing an epigenomic master regulator in cancer

Symbol

Motif

TFClass

TF family

ChIP-Seq AME pval

ChIP-Seq TFT pval

Transcriptomics URA pval

Transcriptomics TFT pval

JUN

TGAGTCA

1.1.1

Jun-related factors

2.85E−16

1.55E−18

2.46E−03

2.40E−17

CEBPB

ATTGC

GCAAT

1.1.8

C/EBP-related

4.04E−40

5.58E−09

0.00E+00

6.38E−09

MYOD

CAGGTG

1.2.2

MyoD / ASC-related factors

1.35E−38

6.97E−18

4.28E−02

6.36E−19

HIF1A

CACGC

1.2.5

PAS domain factors

1.88E−179

3.10E−02

0.00E+00

4.54E−17

SREBF1

CACATG

1.2.6

bHLH-ZIP factors

1.14E−46

1.76E−08

3.81E−02

1.64E−12

MYC

CACATG

1.2.6

bHLH-ZIP factors

9.41E−67

6.24E−21

1.97E−02

6.46E−31

AR

AGAACANNNTCTTGT

2.1.1

Steroid hormone receptors NR3 factors

1.02E−03

2.71E−02

3.30E−02

1.15E−02

SP1

CACCC

2.3.1

Three-zinc finger Krüppel-related factors

4.04E−190

2.40E−63

5.19E−03

9.68E−87

MEIS1

TGACA

3.1.4

TALE-type homeo domain factors

1.90E−04

6.26E−15

7.61E−03

7.37E−12

ZEB1

CACCTG

3.1.8

HD-ZF factors

1.02E−111

4.37E−18

2.88E−02

6.24E−19

ELK1

GGAAG

3.5.2

Ets-related factors

1.97E−03

1.43E−13

2.84E−02

1.78E−24

  1. ChIP-Seq or transcriptomics data provide adjusted p values (pval) using analysis of motif enrichment (AME), transcription factor target analysis (TFT), or up-stream regulator analysis (URA)