Table 4

Over-represented transcription factor binding sites in genes that were differentially expressed after PI 3-kinase inhibition.

Transcription factor

TRANSFAC Matrix

TRANSFAC version

% Genes with site

p-value


Up-regulated genes


Forkhead family members

V$FOXJ2_01

8.4

29

0.004

V$HFH3_01

8.4

29

0.004

V$FOXO1_01

8.4

46

0.007

V$FOXO4_01

8.4

43

0.018

V$HFH1_01

11.1

57

0.001

V$FOXO1_01

11.1

71

0.004

V$FOXO3_01

11.1

75

0.004

V$FOXO1_02

11.1

71

0.006

V$HFH8_01

11.1

57

0.009

V$FOXJ2_01

11.1

43

0.016


Myc/Max

V$MYCMAX_B

8.4

39

0.013

V$MYCMAX_B

11.1

39

0.009


NF-Y

V$NFY_Q6

11.1

46

0.010


Down-regulated genes


NFκB

V$NFKAPPAB65_01

8.4

12

0.017

V$NFKAPPAB_01

11.1

27

0.014


HMGI(Y)

V$HMGIY_Q6

11.1

80

0.014

V$HMGIY_Q3

11.1

73

0.014


The 3 kb regions upstream of the transcription start sites in the human and mouse orthologous sequences were analyzed with the Match algorithm using the MinSUM threshold and both TRANSFAC v8.4 and v11.1 in order to identify over-represented matrices. P-values were calculated using the permutation test and adjusted for multiple testing by FDR correction. Significant matrices were those with p < 0.02 that predicted less than 1 match in 1 kb of sequence in the background set.

Terragni et al. BMC Cell Biology 2008 9:6   doi:10.1186/1471-2121-9-6

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