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

Table 7

The TFs whose known binding motifs cannot be found by MEME/AlignACE/PHYME, but can be found using our method. Three different parameter threshold settings, namely, (a), (b), and (c), are used in our method as given in Table 2.

TF	Genes in PS	Our method	Known motif
Ace2^(b)	1	GCTGGT	TGCTGGT
Hap1^(b)	4	TGCCGNNNNNNNCGG	CGGNNNTANCGG
Mse^(b)	1	GNCACAA	CRCAAAW
Put3^(b)	1	TCGNNNNNNNNNNNCG	CGGNNNNNNNNNNCCG
Swi5^(b)	2	TGCTGG	KGCTGR
Uasino^(b)	1	CATGTG	ATCTGAAWW
Uasphr^(c)	14	TCTNNNNNNNNNNTCCT	CTTCCT