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SpeCond: a method to detect condition-specific gene expression

Florence MG Cavalli1*, Richard Bourgon12, Wolfgang Huber2, Juan M Vaquerizas1 and Nicholas M Luscombe13

Author Affiliations

1 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK

2 Department of Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA

3 EMBL-Heidelberg Genome Biology Unit, Meyerhofstra├če 1, 69117 Heidelberg, Germany

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Genome Biology 2011, 12:R101  doi:10.1186/gb-2011-12-10-r101

Published: 18 October 2011

Abstract

Transcriptomic studies routinely measure expression levels across numerous conditions. These datasets allow identification of genes that are specifically expressed in a small number of conditions. However, there are currently no statistically robust methods for identifying such genes. Here we present SpeCond, a method to detect condition-specific genes that outperforms alternative approaches. We apply the method to a dataset of 32 human tissues to determine 2,673 specifically expressed genes. An implementation of SpeCond is freely available as a Bioconductor package at http://www.bioconductor.org/packages/release/bioc/html/SpeCond.html webcite.