Journal Article

rHVDM: an R package to predict the activity and targets of a transcription factor

M. Barenco, E. Papouli, S. Shah, D. Brewer, C.J. Miller and M. Hubank

in Bioinformatics

Volume 25, issue 3, pages 419-420
Published in print February 2009 | ISSN: 1367-4803
Published online December 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn639
rHVDM: an R package to predict the activity and targets of a transcription factor

More Like This

Show all results sharing this subject:

  • Bioinformatics and Computational Biology

GO

Show Summary Details

Preview

Summary: Highly parallel genomic platforms like microarrays often present researchers with long lists of differentially expressed genes but contain little or no information on how these genes are regulated. rHVDM is a novel R package which uses gene expression time course data to predict the activity and targets of a transcription factor. In the first step, rHVDM uses a small number of known targets to derive the activity profile of a given transcription factor. Then, in a subsequent step, this activity profile is used to predict other putative targets of that transcription factor. A dynamic and mechanistic model of gene expression is at the heart of the technique. Measurement error is taken into account during the process, which allows an objective assessment of the robustness of fit and, therefore, the quality of the predictions. The package relies on efficient algorithms and vectorization to accomplish potentially time consuming tasks including optimization and differential equation integration. We demonstrate the efficiency and accuracy of rHVDM by examining the activity of the tumour-suppressing transcription factor, p53.

Availability: The version of the package presented here (1.8.1) is freely available from the Bioconductor Web site (http://bioconductor.org/packages/2.3/bioc/html/rHVDM.html).

Contact: m.barenco@ucl.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1257 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.