Journal of Probability and Statistics

Research Article

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

Table 6

Comparison to PHYME. For each TF, we listed the number of predicted motifs and 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.
TFKnown motifFound by our methodRankFound by PHYMERank
Ste12(a)TGAAACATGAAACA1TGAAACA3
Gal4(a)CGGNNNNNNNNNNNCCGCGGNNNNNNNNNNNCCG1CCGAATAGTCTGCCCCG8
Mbp1(a)ACGCGTNAACGCGT1ACGCGTCA3
Leu3(a)CCGGNNCCGGCGGNNNCGG1CCGGTACCGG3
Cbf1(a)RTCACRTGCACGTG2GTCACGTG2
MET31(a)CTGTGGCTGTGGC1Not found
Abf1(b)TCRNNNNNNACGTCANNNNNNACG3Not found
Ace2(b)GCTGGTTGCTGGT2Not found
Gcn4(b)TGANTNATGACT6TGAGTC6
Hap1(b)CGGNNNTANCGGTGCCGNNNNNNNCGG1Not found
Ino4(b)CATGTGAAATCATGTT4Not found
Mcb(b)WCGCGWCGCNTCG1ACGCGT1
Mse(b)CRCAAAWGACNCAA5CACAAAA3
Nbf(b)ATGYGRAWWCATGTG15ATGTGAAAT1
Pdr3(b)TCCGYGGATCCNNGGA1TCCGCGGA2
Pho4(b)CACGTKGCGCGT1Not found
Put3(b)CGGNNNNNNNNNNCCGTCGNNNNNNNNNNNCG1Not found
Rap1(b)RMACCCAGTCNNNNNCCCAT11AAACCGA4
Swi5(b)KGCTGRTGCTGG1TGCTGAATG1
Uasino(b)ATCTGAAWWCATGTG13Not found
Uasrad(b)WTTTCCCGSTCCNGCT3TTTCCCAC4
Adr1(c)TCTCCCTCCNNNNNTCC2ACTCC4
Mig1(c)CCCCRNNWWWWWACCCCA30CCCCGCCCC4
Uasphr(c)CTTCCTTCTNNNNNNNNNNTCCT13GCTTTCTTT8
T4c(c)TTTTCTYCGTTTTCNNNNNTCC6TTTTTCTTTT1
Ap-1TTANTAANot foundNot found
Bas2TAATRA,TAANTAANot foundTAATAG8
CsreYCGGAYRRAWGGNot foundNot found
Mac1GAGCAAANot foundGAGAAAA3
Gcr1CWTCCNot foundNot found
Mcm1CCNNNWWRGGNot foundCCGTTTTGGG5
Reb1YYACCCGNot foundCTACCCG5
Rox1YYNATTGTTYNot foundNot found
ScbCNCGAAANot foundCACGAAA1
SffGTMAACAANot foundGTTAACAA6