rHVDM: an R package to predict the activity and targets of a transcription factor.
AffiliationInstitute of Child Health, University College London, 30 Guilford street, London WC1N 1EH, UK. firstname.lastname@example.org
MetadataShow full item record
AbstractSUMMARY: 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).
CitationrHVDM: an R package to predict the activity and targets of a transcription factor. 2009, 25 (3):419-20 Bioinformatics
- oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language.
- Authors: Sanges R, Cordero F, Calogero RA
- Issue date: 2007 Dec 15
- Regulatory motif finding by logic regression.
- Authors: Keles S, van der Laan MJ, Vulpe C
- Issue date: 2004 Nov 1
- rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.
- Authors: Droit A, Cheung C, Gottardo R
- Issue date: 2010 Mar 1
- tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor.
- Authors: Honkela A, Gao P, Ropponen J, Rattray M, Lawrence ND
- Issue date: 2011 Apr 1
- Targetfinder.org: a resource for systematic discovery of transcription factor target genes.
- Authors: Kiełbasa SM, Blüthgen N, Fähling M, Mrowka R
- Issue date: 2010 Jul