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

Table 3

Comparison to AlignACE. 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	AlignACE		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)	11	2	1	1
Gal4^(a)	9	2	1	1
Leu3^(a)	22	3	1	1
Mbp1^(a)	20	7	2	1
Cbf1^(a)	29	1	4	2
Met31^(a)	20	15	1	1
Abf1^(b)	10	4	5	3
Ace2^(b)	7	Not found	4	2
Gcn4^(b)	11	4	39	6
Hap1^(b)	6	Not found	23	1
Ino4^(b)	13	Not found	22	4
Mcb^(b)	18	2	11	1
Mse^(b)	6	Not found	5	5
Nbf^(b)	6	1	16	15
Pdr3^(b)	12	Not found	10	2
Pho4^(b)	8	Not found	9	1
Put3^(b)	2	Not found	4	1
Rap1^(b)	13	6	14	11
Swi5^(b)	9	Not found	3	1
Uasino^(b)	4	Not found	14	13
Uasrad^(b)	4	Not found	20	3
Adr1^(c)	4	2	14	2
Mig1^(c)	30	2	32	30
Uasphr^(c)	14	Not found	47	13
T4c^(c)	9	1	28	6