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

BMC Genomics

Table 12 Identification of DNA motifs in CUX1 binding sites without the ATCRATconsensus

Motif	Reverse complement	E-Value	Transcription factors
DTATTTW	WAAATAH	3.80E-35	-
CYCCRCCC	GGGYGGRG	4.60E-34	Klf4, Klf7, Sp1, Sp4, Zfp281, Zfp740, Egr1
CAYTTCY	RGAARTG	1.50E-26	Gabpa, Stat1
CACASAS	STSTGTG	3.20E-23	Runx1
DGGAAA	TTTCCH	5.00E-22	Stat1, Nfatc2, Rela, Rel, Fev
CCRCCDCC	GGHGGYGG	6.40E-19	-
GSAGAGR	YCTCTSC	3.90E-17	-
CHGCAGC	GCTGCDG	1.30E-16	Myf, Ascl2
CATTTWM	KWAAATG	2.90E-26	-
DTTTCTS	SAGAAAH	1.70E-13	-

10 Most enriched DNA motifs found in CUX1 binding sites that do notcontain the ATCRAT CUX1 consensus. The DNA sequences considered inthis analysis correspond to the entire regions bound by CUX1 asdefined in the microarray. The size of bound regions varies from 149to 949 bp (95^th percentile) and is 477 bp onaverage. Proteins with DNA binding motifs highly similar to themotifs are listed in the rightmost column.

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