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

Table 2

Comparison between the known motifs and the motifs found using our method. Different parameter threshold settings are used in our motif finding. (a) P-value in a magnitude of 10⁻⁶ (after Bonferroni adjustment), ARE_𝑝=1.0, and Z-value = 2.0; (b) P-value = 0.01 (without Bonferroni adjustment), ARE_𝑝=1.0, and Z-value = 2.0; (c) P-value = 0.01 (without Bonferroni adjustment), ARE_𝑝=0.8, and Z-value = 2.0.

TF	Genes in PS	Known motif	Motif found	P-value	Z-value	ARE𝑝
Ste12^(a)	9	TGAAACA	TGAAACA	5.6𝑒−12	3.68	1.00
Gal4^(a)	10	CGGNNNNNNNNNNNCCG	CGGNNNNNNNNNNNCCG	3.7𝑒−12	2.43	1.22
Mbp1^(a)	18	ACGCGTNA	ACGCGT	3.0𝑒−7	3.37	1.35
Leu3^(a)	10	CCGGNNCCGG	CGGNNNCGG	7.0𝑒−13	3.15	1.27
Cbf1^(a)	16	RTCACRTG	CACGTG	7.7𝑒−13	2.98	1.19
MET31^(a)	8	CTGTGGC	TGTGGC	6.7𝑒−7	3.39	1.06
Abf1^(b)	15	TCRNNNNNNACG	TCANNNNNNACG	1.3𝑒−3	3.73	1.26
Ace2^(b)	1	GCTGGT	TGCTGGT	1.4𝑒−3	6.07	1.55
Gcn4^(b)	6	TGANTN	ATGACT	8.7𝑒−4	4.45	1.10
Hap1^(b)	4	CGGNNNTANCGG	TGCCGNNNNNNNCGG	2.3𝑒−4	6.09	1.64
Ino4^(b)	6	CATGTGAAAT	CATGTT	2.9𝑒−4	5.60	1.31
Mcb^(b)	6	WCGCGW	CGCNTCG	4.1𝑒−4	4.66	1.36
Mse^(b)	1	CRCAAAW	GACNCAA	8.3𝑒−3	4.05	1.19
Nbf^(b)	1	ATGYGRAWW	CATGTG	5.9𝑒−3	5.85	1.36
Pdr3^(b)	2	TCCGYGGA	TCCNNGGA	4.3𝑒−4	2.88	1.03
Pho4^(b)	2	CACGTK	GCGCGT	1.8𝑒−3	3.55	1.20
Put3^(b)	1	CGGNNNNNNNNNNCCG	TCGNNNNNNNNNNNCG	2.6𝑒−4	4.65	1.51
Rap1^(b)	8	RMACCCA	GTCNNNNNCCCAT	8.8𝑒−3	3.16	1.01
Swi5^(b)	2	KGCTGR	TGCTGG	6.5𝑒−4	4.45	1.19
Uasino^(b)	1	ATCTGAAWW	CATGTG	5.9𝑒−3	5.83	1.36
Uasrad^(b)	2	WTTTCCCGS	TCCNGCT	1.1𝑒−3	4.42	1.24
Adr1^(c)	2	TCTCC	CTCCNNNNNTCC	1.6𝑒−3	2.18	0.88
Mig1^(c)	7	CCCCRNNWWWWW	ACCCCA	7.2𝑒−3	2.18	0.82
Uasphr^(c)	14	CTTCCT	TCTNNNNNNNNNNTCCT	2.2𝑒−3	2.38	0.93
T4c^(c)	2	TTTTCTYCG	TTTTCNNNNNTCC	1.2𝑒−3	2.69	0.96