Table 1

PWM pairs with high and low FR values in the genomic set of promoters.

Transcription factor A (PWM ID)

Transcription factor B (PWM ID)

FRgenomic(B|A) (high/low) *

Species

GC content difference


TBP (M00471)

Six6 (PB0163)

2.75 (high)

human

0.28

Six6 (PB0163)

TBP (M00471)

2.56 (high)

human

0.28

POU1F1, POU3F2 (M00463)

Six6 (PB0163)

2.10 (high)

mouse

0.22

TBP (M00471)

POU2F1, Sox15 (M00162)

2.09 (high)

mouse

0.21

POU2F1, Sox15 (M00162)

TBP (M00471)

2.08 (high)

mouse

0.21

TBP (M00471)

Cux1 (PH0017)

2.07 (high)

mouse

0.22

Six6 (PB0163)

POU1F1, POU3F2 (M00463)

2.06 (high)

mouse

0.22

Six6 (PB0163)

TBP (M00471)

1.89 (high)

mouse

0.28

various homeobox TFs (PH0077)

TBP (M00471)

1.88 (high)

mouse

0.27

Sox17, Sox8 (PB0178)

TBP (M00471)

1.80 (high)

mouse

0.28

Zfp105 (PB0197)

TBP (M00471)

1.80 (high)

mouse

0.29

TBP (M00471)

Six6 (PB0163)

1.79 (high)

mouse

0.28

TBP (M00471)

Sox17, Sox8 (PB0178)

1.79 (high)

mouse

0.28

TBP (M00471)

various homeobox TFs (PH0077)

1.76 (high)

mouse

0.27

TBP (M00471)

Zfp105 (PB0197)

1.75 (high)

mouse

0.29

C/EBP factors (M00201)

TBP (M00471)

1.53 (high)

mouse

0.34

MITF-TFE family (bHLH) (M01029)

E2F TFs (M00516)

0.65 (low)

mouse

0.12

E2F TFs (PB0009)

MITF-TFE family (bHLH) (M01029)

0.54 (low)

mouse

0.15


* (high/low) indicates whether the genomic FR is higher or lower than expected.

Vandenbon et al. BMC Genomics 2012 13(Suppl 7):S11   doi:10.1186/1471-2164-13-S7-S11

Open Data