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

Barenco, M, Papouli, E, Shah, S, Brewer, D, Miller, C J and Hubank, M (2009) rHVDM: an R package to predict the activity and targets of a transcription factor. Bioinformatics, 25 (3). pp. 419-420. ISSN 1460-2059

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Abstract

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.

Item Type: Article
Uncontrolled Keywords: algorithms,gene expression profiling,internet,software,transcription factors,tumor suppressor protein p53
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Pure Connector
Date Deposited: 06 Jan 2014 14:16
Last Modified: 21 Apr 2020 22:43
URI: https://ueaeprints.uea.ac.uk/id/eprint/47034
DOI: 10.1093/bioinformatics/btn639

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