Measuring similarities between transcription factor binding sites.
BACKGROUND
Collections of transcription factor binding profiles (Transfac, Jaspar) are essential to identify regulatory elements in DNA sequences. Subsets of highly similar profiles complicate large scale analysis of transcription factor binding sites.


RESULTS
We propose to identify and group similar profiles using two independent similarity measures: chi2 distances between position frequency matrices (PFMs) and correlation coefficients between position weight matrices (PWMs) scores.


CONCLUSIONS
We show that these measures complement each other and allow to associate Jaspar and Transfac matrices. Clusters of highly similar matrices are identified and can be used to optimise the search for regulatory elements. Moreover, the application of the measures is illustrated by assigning E-box matrices of a SELEX experiment and of experimentally characterised binding sites of circadian clock genes to the Myc-Max cluster.
Kielbasa
Szymon M
SM
Institute for Theoretical Biology, Humboldt University, Invalidenstrasse 43, D-10115 Berlin, Germany. s.kielbasa@biologie.hu-berlin.de
Gonze
Didier
D
Herzel
Hanspeter
H
D056930:ARNTL Transcription Factors; D051792:Basic Helix-Loop-Helix Proteins / Q000378:metabolism; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D002940:Circadian Rhythm / Q000235:genetics; D030561:Databases, Nucleic Acid; D024721:E-Box Elements / Q000502:physiology; D008954:Models, Biological; D009711:Nucleotides / Q000032:analysis; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D014157:Transcription Factors / Q000378:metabolism*
D056930:ARNTL Transcription Factors; D051792:Basic Helix-Loop-Helix Proteins; D009711:Nucleotides; D014157:Transcription Factors