BIROn - Birkbeck Institutional Research Online

Variable structure motifs for transcription factor binding sites

Reid, J.E. and Evans, Kenneth J. and Dyer, N. and Wernisch, Lorenz and Ott, S. (2010) Variable structure motifs for transcription factor binding sites. BMC Genomics 11 (1), p. 30. ISSN 1471-2164.

[img]
Preview
Text
3263.pdf - Published Version of Record
Available under License Creative Commons Attribution.

Download (2MB) | Preview

Abstract

Classically, models of DNA-transcription factor binding sites (TFBSs) have been based on relatively few known instances and have treated them as sites of fixed length using position weight matrices (PWMs). Various extensions to this model have been proposed, most of which take account of dependencies between the bases in the binding sites. However, some transcription factors are known to exhibit some flexibility and bind to DNA in more than one possible physical configuration. In some cases this variation is known to affect the function of binding sites. With the increasing volume of ChIP-seq data available it is now possible to investigate models that incorporate this flexibility. Previous work on variable length models has been constrained by: a focus on specific zinc finger proteins in yeast using restrictive models; a reliance on hand-crafted models for just one transcription factor at a time; and a lack of evaluation on realistically sized data sets.

Metadata

Item Type: Article
School: Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences
Depositing User: Administrator
Date Deposited: 05 Apr 2011 14:49
Last Modified: 18 Jul 2025 02:42
URI: https://eprints.bbk.ac.uk/id/eprint/3263

Statistics

6 month trend
435Downloads
6 month trend
254Hits

Additional statistics are available via IRStats2.

Archive Staff Only (login required)

Edit/View Item
Edit/View Item