Skip to main content

Table 1 Analysis for over-representation of transcription factor binding sites using the PRIMO

From: Mapping of HNF4α target genes in intestinal epithelial cells

  

HNF4α ChIP-chip data

Caco2 mRNA expression data

Acc. No1

Transcription factor

Hits2

P-value

Hits2

P-value

M00411

HNF-4alpha1

(3161,18621,452,1089)

1.3E-43

(3296,18493,317,1217)

1.1E-05

M00134

HNF-4

(3294,18488,453,1088)

1.7E-39

(3428,18361,319,1215)

2.2E-04

M00158

COUP-TF, HNF-4

(3343,18439,421,1120)

4.8E-28

(3439,18350,325,1209)

4.1E-05

M00803

E2F

(10649,11133,984,557)

2.0E-27

(10787,11002,846,688)

1.0E-02

M00464

POU3F2

(2673,19109,59,1482)

9.6E-27

(2649,19140,83,1451)

2.4E-15

M00764

HNF-4 direct repeat 1

(3511,18271,418,1123)

5.0E-23

(3613,18176,316,1218)

3.8E-02

M00512

PPARG

(2775,19007,340,1201)

1.5E-19

(2888,18901,227,1307)

1

M00196

Sp1

(8570,13212,777,764)

1.2E-14

(8580,13209,767,767)

2.5E-13

M00108

NRF-2

(2787,18995,321,1220)

1.6E-14

(2937,18852,171,1363)

1

M00932

Sp1

(8850,12932,795,746)

2.7E-14

(8875,12914,770,764)

2.9E-10

M00931

Sp1

(8375,13407,757,784)

1.1E-13

(8377,13412,755,779)

7.6E-14

M00762

PPAR, HNF-4, COUP, RAR

(3936,17846,412,1129)

2.9E-13

(3999,17790,349,1185)

1.5E-02

M00025

Elk-1

(2235,19547,264,1277)

1.4E-12

(2340,19449,159,1375)

1

M00695

ETF

(7391,14391,674,867)

6.9E-12

(7446,14343,619,915)

5.7E-04

M00933

Sp1

(9528,12254,828,713)

1.7E-11

(9544,12245,812,722)

2.1E-09

M00638

HNF-4alpha

(2389,19393,271,1270)

5.5E-11

(2419,19370,241,1293)

7.5E-05

M00032

c-Ets-1(p54)

(2633,19149,291,1250)

8.8E-11

(2730,19059,194,1340)

1

M00763

PPAR direct repeat 1

(3802,17980,387,1154)

1.8E-10

(3860,17929,329,1205)

1.5E-01

M00765

COUP direct repeat 1

(3324,18458,336,1205)

2.9E-08

(3390,18399,270,1264)

1

M00672

TEF

(3512,18270,161,1380)

3.4E-07

(3512,18277,161,1373)

5.0E-07

M00341

GABP

(3601,18181,347,1194)

2.4E-06

(3699,18090,249,1285)

1

M00287

NF-Y

(3353,18429,327,1214)

2.6E-06

(3382,18407,298,1236)

3.8E-02

M00652

Nrf-1

(2721,19061,273,1268)

6.3E-06

(2790,18999,204,1330)

1

M00255

GC box

(9746,12036,803,738)

1.1E-05

(9751,12038,798,736)

1.9E-05

M00430

E2F-1

(2322,19460,236,1305)

3.8E-05

(2369,19420,189,1345)

1

M00224

STAT1

(2188,19594,223,1318)

7.3E-05

(2246,19543,165,1369)

1

M00716

ZF5

(6120,15662,528,1013)

1.8E-04

(6167,15622,481,1053)

1

M00649

MAZ

(9648,12134,782,759)

4.6E-04

(9670,12119,760,774)

4.6E-02

M00309

ACAAT

(3028,18754,286,1255)

5.2E-04

(3056,18733,258,1276)

1

M00775

NF-Y

(2771,19011,265,1276)

5.6E-04

(2793,18996,243,1291)

4.8E-01

M00008

Sp1

(7119,14663,593,948)

1.8E-03

(7071,14718,641,893)

8.1E-11

M00007

Elk-1

(2809,18973,258,1283)

1.4E-02

(2851,18938,216,1318)

1

M00225

STAT3

(2167,19615,206,1335)

1.7E-02

(2205,19584,168,1366)

1

M00778

AhR

(891,20891,98,1443)

3.0E-02

(924,20865,65,1469)

1

M00084

MZF1

(4944,16838,419,1122)

3.4E-02

(4985,16804,378,1156)

1

  1. Analysis for over-representation of transcription factor binding sites using the PRIMO program on the HNF4α target promoters (HNF4α ChIP-chip data), and on the promoters of genes that are up-regulated during intestinal cell differentiation (Caco-2 mRNA expression data).
  2. 1 Accession numbers are obtained from Transfac database http://www.biobase.de. 2 The numbers in the parentheses referrers to: The first number = transcription factor binding site (TFBS)-positive promoters in the background set of promoters on the NimbleGen promoter array. The second number = TFBS-negative promoters in the background set of promoters analyzed on the NimbleGen promoter array. The third number = TFBS-positive promoters in the target set of promoters. The fourth number = TFBS-negative promoters in target set of promoters. The background set contains all promoters on the Nimblegen promoter array except the promoters represented in the target set. The target sets of promoters are promoters predicted to associate with HNF4α or promoters up-regulated during Caco-2 differentiation. P-value is calculated using Fisher's Exact test and Bonferroni correction for multiple testing.