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

Table 4

Comparison to MEME. MEME requests a predetermined number of predicted motifs as its input, and we let it be the number of motifs predicted using our method. For each TF, we listed the rank of the known motif in the predictions. Three different parameter threshold settings, namely, (a), (b), and (c), are used in our method as given in Table 2.

TF	Meme		Our Method
	The number of motifs found	The rank of the known motif	The number of motifs found	The rank of the known motif
Ste12(^a)	1	Not found	1	1
Gal4^(a)	1	1	1	1
Leu3^(a)	1	1	1	1
Mbp1^(a)	2	1	2	1
Cbf1^(a)	4	1	4	2
Met31^(a)	1	Not found	1	1
Abf1^(b)	5	Not found	5	3
Ace2^(b)	4	Not found	4	2
Gcn4^(b)	39	Not found	39	6
Hap1^(b)	9	Not found	23	1
Ino4^(b)	22	10	22	4
Mcb^(b)	11	1	11	1
Mse^(b)	5	Not found	5	5
Nbf^(b)	16	3	16	15
Pdr3^(b)	10	1	10	1
Pho4^(b)	9	4	9	1
Put3^(b)	4	Not found	4	1
Rap1^(b)	14	Not found	14	11
Swi5^(b)	3	Not found	3	1
Uasino^(b)	14	Not found	14	13
Uasrad^(b)	20	1	20	3
Adr1^(c)	10	Not found	14	2
Mig1^(c)	32	2	32	30
Uasphr^(c)	47	Not found	47	13
T4c^(c)	28	23	28	6