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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.