Annotating significant pairs of transcription factor binding sites in 
regulatory DNA

Rateitschak, Katja; Mueller, Tobias; Vingron, Martin

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Annotating significant pairs of transcription factor binding sites in regulatory DNA

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Rateitschak, Katja
Max Planck Society;

Mueller, Tobias
Max Planck Society;

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Vingron, Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Rateitschak, K., Mueller, T., & Vingron, M. (2004). Annotating significant pairs of transcription factor binding sites in regulatory DNA. Special Issue: Ontology Workshop Tokyo 2003, 0040-0040.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-87E9-B

Abstract

In the presented work we search for transcription factor binding sites (BS) by including additional information about typical BS patterns. The new proposed score combines the ordinary profile score based on TRANSFAC-matrices together with a score based on pairs of BS. The latter score positively weights pairs of BS that tend to occur together in many regulatory DNA-sequences, in contrast to a random background model. The empirical BS pair frequencies result from our evaluation of a large dataset of orthologous genes.