EXMOTIF: efficient structured motif extraction

Table 5 Regulons of Zn cluster proteins.

TF Name	Known Motif	Predicted Motifs	Num-Motifs	Ranking
GAL4 GAL4 chips	CGGRnnRCYnYnCnCCG	CGG[11,11]CCG	1634(3346)	1/1
CAT8	CGGnnnnnnGGA	CGG[6,6]GGA	1621(3356)	147/13
HAP1	CGGnnnTAnCGGCGGnnnTAnCGGnnnTA	CGG[6,6]CGG	1621(3356)	111/146
LEU3	RCCGGnnCCGGY	CCG[4,4]CGG	1588(3366)	2/1
LYS	WWWTCCRnYGGAWWW	TCC[3,3]GGA	1605(3360)	33/21
PPR1	WYCGGnnWWYKCCGAW	CGG[6,6]CCG	1621(3356)	1/2
PUT3	YCGGnAnGCGnAnnnCCGA CGGnAnGCnAnnnCCGA	CGG[10,11]CCG	727(4035)	1/1

TF Name stands for transcription factor name; Known Motif stands for the known binding sites corresponding to the transcription factors in TF Name column; Predicted Motifs stands for the motifs predicted by EXMOTIF; Num-Motifs gives the final (original) number of motifs extracted (final is after pruning those motifs that are also frequent in the ORF regions); Ranking stands for the Z-score ranking based on support/weighted support.

ISSN: 1748-7188