Finding Transcription Factor Binding Motifs for Coregulated Genes by Combining Sequence Overrepresentation with Cross-Species Conservation

Table 5

The TFs whose known binding sites cannot be found using our method. The expected number of motifs predicted by MEME was set at 10.

TF	Known motif	Using AlignACE	Rank of the known motif/total predictions	Using MEME	Rank of the known motif/total predictions
Ap-1	TTANTAA	Not found		TTAGTAA	3/10
Bas2	TAATRA,TAANTAA	Not found		Not found
Csre	YCGGAYRRAWGG	Not found		GTCCGGAC	8/10
Mac1	GAGCAAA	GGAAGCAAA	17/33	Not found
Gcr1	CWTCC	ATTGTTTTCC	5/5	Not found
Mcm1	CCNNNWWRGG	TTACCNNNTAGGAAA	2/11	TTTCCTAATTAGGAAA	1/10
Reb1	YYACCCG	TTACCCGCACGGC	3/8	Not found
Rox1	YYNATTGTTY	Not found		Not found
Scb	CNCGAAA	AAGCCACGAAAA	1/13	Not found
Sff	GTMAACAA	Not found		Not found