tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor

Antti Honkela; Pei Gao; Jonatan Ropponen; Magnus Rattray; Neil D Lawrence

doi:10.1093/bioinformatics/btr057

tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor

Bioinformatics. 2011 Apr 1;27(7):1026-7. doi: 10.1093/bioinformatics/btr057. Epub 2011 Feb 7.

Authors

Antti Honkela¹, Pei Gao, Jonatan Ropponen, Magnus Rattray, Neil D Lawrence

Affiliation

¹ Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland. antti.honkela@hiit.fi

PMID: 21300702
DOI: 10.1093/bioinformatics/btr057

Abstract

tigre is an R/Bioconductor package for inference of transcription factor activity and ranking candidate target genes from gene expression time series. The underlying methodology is based on Gaussian process inference on a differential equation model that allows the use of short, unevenly sampled, time series. The method has been designed with efficient parallel implementation in mind, and the package supports parallel operation even without additional software.

Availability: The tigre package is included in Bioconductor since release 2.6 for R 2.11. The package and a user's guide are available at http://www.bioconductor.org.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling
Gene Expression Regulation
Oligonucleotide Array Sequence Analysis
Software*
Transcription Factors / metabolism*

Substances

Transcription Factors