Table 1 |
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Over-represented TFBSs in GRB target promoters |
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Background: bystander gene promoters |
Background: other CpG island promoters |
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|
|
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|
Family |
Name |
Hit p-value |
Sequence occurrence p-value |
Hit p-value |
Sequence occurrence p-value |
|
|
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|
FORKHEAD |
Foxa2 |
0.009 |
0.0001 |
0.0001 |
0.0001 |
|
FORKHEAD |
Foxd3 |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
FORKHEAD |
FOXI1 |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
FORKHEAD |
FOXL1 |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
FORKHEAD |
Foxq1 |
0.0001 |
0.0001 |
0.0002 |
0.0001 |
|
ZN-FINGER, C2H2 |
Gfi |
0.0068 |
0.0001 |
0.0001 |
0.0001 |
|
HOMEO |
Lhx3 |
0.0003 |
0.0001 |
0.0001 |
0.0001 |
|
MADS |
MEF2A |
0.0001 |
0.0001 |
0.0008 |
0.0001 |
|
HOMEO |
Nkx2-5 |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
HOMEO |
Nobox |
0.0002 |
0.0001 |
0.0001 |
0.0001 |
|
HOMEO |
Pdx1 |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
HOMEO |
Prrx2 |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
ZN-FINGER, C2H2 |
RREB1 |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
HMG |
Sox5 |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
HMG |
SOX9 |
0.0025 |
0.0001 |
0.0005 |
0.0001 |
|
HMG |
SRY |
0.0001 |
0.0001 |
0.0001 |
0.0001 |
|
HOMEO |
TCF1 |
0.0017 |
0.0001 |
0.0001 |
0.0001 |
|
|
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|
TFBS content of target gene promoters was compared to two different background sets. The ones over-represented in both comparisons are output in the table. Two distinct p-values represent the significance of the number of profile hits in the target set (hit p-value) and the significance of the number of sequences having at least one hit in the target set (sequence occurrence p-value). |
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|
Akalin et al. Genome Biology 2009 10:R38 doi:10.1186/gb-2009-10-4-r38 |
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