Table 1

Transcription factor binding site enrichment in clusters

Cluster

TFBS

Promoter range [kb]a

Gene hits

Z-scoreb

Fisher scoreb


1 (local, 936 DEG)

RELA

-5/5

244

20.45

7.97E-05

NF-kappaB

-5/5

287

12.30

2.94E-04

REL

-2/0

206

19.26

4.04E-04

ELF5

-5/5

530

16.69

5.71E-04

STAT1

-5/5

119

12.44

5.84E-04

SRF

-5/5

48

12.10

8.09E-04

SPIB

-2/2

502

11.23

2.09E-03

Fos

-5/2

393

10.51

2.90E-03


2 (systemic, 703 DEG)

NFIL3

-2/2

100

12.72

4.53E-03

TP53

-5/2

3

13.36

3.87E-02

HLF

-2/2

127

13.06

4.23E-02


3 (systemic, 367 DEG)

FOXD1

-2/2

128

13.09

5.19E-07

Foxa2

-5/2

158

12.46

2.75E-06

Fos

-2/2

146

13.04

2.77E-05

Pdx1

-2/0

156

23.12

3.63E-05

FOXI1

-2/0

93

14.90

9.69E-05

SRY

-5/2

192

18.15

1.55E-04

PBX1

-2/0

29

11.26

1.97E-04

REL

-2/0

92

10.49

2.57E-04

Foxd3

-5/2

150

12.46

8.87E-04

Sox5

-5/2

192

12.63

9.38E-04

Nkx2-5

-2/2

188

23.31

9.98E-04

Lhx3

-2/0

81

14.12

1.10E-03

Prrx2

-2/2

174

20.48

1.91E-03

NFIL3

-5/2

78

10.24

1.37E-04


4 (systemic, 41 DEG)

PBX1

-2/2

9

10.26

1.89E-03

STAT1

-5/2

9

12.03

7.36E-03


5 (systemic, 36 DEG)

HNF4A

-2/0

7

10.21

4.44E-02

NR2F1

-2/0

4

12.14

9.58E-02


6 (local, 252 DEG)

Hand1-Tcfe2a

-2/2

129

10.40

2.31E-07


a range of the considered promoter region in the human ortholog upstream (-) or downstream of the transcription start site (TSS)

branking metrics for TFBS overrepresentation, Z-score accounts for frequency and Fisher-score for presence/absence of a given TFBS

Mitterhuemer et al. BMC Genomics 2010 11:138   doi:10.1186/1471-2164-11-138

Open Data