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Bioinformatics Advance Access published online on April 26, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti461
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received January 20, 2005
Revised March 18, 2005
Accepted April 21, 2005

Applications note

TFBScluster: a resource for the characterisation of transcriptional regulatory networks

Ian John Donaldson 1, Michael Chapman 1, and Berthold Göttgens 1*

1 Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK

* To whom correspondence should be addressed.
Berthold Göttgens, E-mail: bg200{at}cam.ac.uk


  Abstract

One major challenge of the post-sequencing era of the human genome project will be the functional annotation of the non-coding portion of the genome, in particular gene regulatory sequences. We have developed a new web-based tool, TFBScluster, which performs genome-wide identification of transcription factor binding site clusters that are conserved in multiple mammalian genomes. Clusters representing candidate gene regulatory elements can be filtered further based on the presence or absence of additional user defined DNA sequence motifs, or by constraining the orientation or order of binding sites. Comprehensive results files, returned by email, are designed to facilitate experimental validation of computationally identified candidate gene regulatory sequences. TFBScluster therefore has the potential to contribute to deciphering transcriptional networks that regulate a wide range of mammalian developmental processes.

Availability: http://hscl.cimr.cam.ac.uk/TFBScluster_genome_34.html.

Supplementary information: http://hscl.cimr.cam.ac.uk/sup_don05_app_api.html.


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