Long-range transcriptional regulation by the p110 CUX1 homeodomain protein on theENCODE array

BMC Genomics

Table 11 Identification of DNA motifs in CUX1 binding sites with the ATCRATconsensus

Motif	Reverse complement	E-Value	Transcription factors
ATCRAT	ATYGAT	3.5E-735	Cux1, Pbx1
GGGYGGGR	YCCCRCCC	4.8E-35	Klf4, Klf7, Sp1, Sp4, Zfp281, Zfp740, Egr1
AAATAHW	WDTATTT	1.9E-27	-
CTBCCTS	SAGGVAG	6.30E-26	Spi1, Stat3, Fev, Sfpi1
CWCCDCC	GGHGGWG	6.60E-23	-
DRGGAAA	TTTCCYH	6.20E-21	-
BSTGTGTG	CACACASV	1.20E-20	-
RGAGAAR	YTTCTCY	2.60E-14	-
ACRCWG	CWGYGT	3.70E-14	-
RAAACAAA	TTTGTTTY	1.90E-11	Sox11, Sox4, Foxd3, Foxi1

10 Most enriched DNA motifs found in CUX1 binding sites that containthe ATCRAT CUX1 consensus. The DNA sequences considered in thisanalysis correspond to the entire regions bound by CUX1 as definedin the microarray. The size of bound regions varies from 149 to1107 bp (95^th percentile) and is 532 bp onaverage. Proteins with DNA binding motifs highly similar to themotifs are listed in the rightmost column. K = G/T,M = A/C, R = A/G, Y = C/T,S = C/G, W = A/T, B = C/G/T,V = A/C/G, H = A/C/T,D = A/G/T.

ISSN: 1471-2164