Measuring similarities between transcription factor binding sites.

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

SUBMITTER: Kielbasa SM 

PROVIDER: S-EPMC1261160 | biostudies-literature | 2005 Sep

REPOSITORIES: biostudies-literature