Measuring similarities between transcription factor binding sites.
Ontology highlight
ABSTRACT: 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.Conclusion
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.
SUBMITTER: Kielbasa SM
PROVIDER: S-EPMC1261160 | biostudies-literature | 2005 Sep
REPOSITORIES: biostudies-literature
Publications
Measuring similarities between transcription factor binding sites.
Kielbasa Szymon M SM Gonze Didier D Herzel Hanspeter H
BMC bioinformatics 20050928
<h4>Background</h4>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.<h4>Results</h4>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) scor ...[more]
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