MoTeX-II: structured MoTif eXtraction from large-scale datasets

BMC Bioinformatics

Table 6 Extraction of transcription factors for the Zinc factors by EXMOTIF and MoTeX-II

			EXMOTIF		MoTeX-II
TF name	Known motif	Predicted Motif	Extracted motifs	Ranking	Extracted motifs	Ranking
GAL4
GAL4 chips	CGGRnnRCYnYnCnCCG	CGG[11,11]CCG	1634(3346)	1/1	1634(3346)	1/1
CAT8	CGGnnnnnnGGA	CGG[6,6]GGA	1621(3356)	451/73	1621(3356)	359/51
HAP1	CGGnnnTAnCGGCGGnnnTAnCGGnnnTA	CGG[6,6]CGG	1621(3356)	84/96	1621(3356)	73/85
LEU3	RCCGGnnCCGGY	CCG[4,4]CGG	1588(3366)	2/2	1588(3366)	1/2
LYS	WWWTCCRnYGGAWWW	TCC[3,3]GGA	1605(3360)	39/25	1605(3360)	32/17
PPR1	WYCGGnnWWYKCCGAW	CGG[6,6]CCG	1621(3356)	1/2	1621(3356)	1/2
PUT3	YCGGnAnGCGnAnnnCCGA
	CGGnAnGCnAnnnCCGA	CGG[10,11]CCG	727(4035)	1/1	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 Motif stands for the motifs extracted by EXMOTIF and MoTeX-II, respectively; Extracted motifs gives the final (original) number of motifs extracted (original is before excluding the motifs that are also valid in the ORF regions); Ranking stands for the z-score ranking based on support/weighted support.
The extraction of transcription factors for the Zinc factors by EXMOTIF and MoTeX-II.

ISSN: 1471-2105