Inference of transcriptional regulation using gene expression data from the bovine and human genomes

BMC Genomics

Table 1 Summary of the identified promoter motifs in Wasserman-Fickett muscle genes of group a

Motif (Seqs; Sites)	Best hit	Score (S)	p-value (P)	CorrectedP
a1 (42; 31)	MEF2_Q6_01 (12)	0.30	0.00	0.00
	MEF2* (10)	0.68	5.00 × 10^-3	0.03
a2 (42; 29)	CHCH_01 (6)	0.99	3.60 × 10^-2	0.09
	SP1_Q6 (13)	0.90	3.70 × 10^-1	0.37
	SP1_Q2_01 (10)	0.96	3.64 × 10^-1	0.37
a4 (11; 7)	POU6F1_01 (11)	0.77	2.00 × 10^-2	0.07
a5 (7; 9)	Myf* (12)	1.21	3.00 × 10^-3	0.04
a15 (6; 6)	TEL2_Q6 (10)	0.19	0.00	0.00
	ETS_Q4 (12)	0.80	0.00	0.00

Sequences in the muscle-specific gene set were examined with MEME for de novo prediction of motifs. The resulting motifs were subsequently compared to entries in the TRANSFAC and JASPAR databases for identification. For each identified motif, the dissimilarity score (S) and the p-value (P) are shown. Corrected p-value for each match is based on an estimated FDR of 10%. Matches to the JASPAR database are marked by (*).

ISSN: 1471-2164