SpeCond: a method to detect condition-specific gene expression.
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.
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK. florence@ebi.ac.uk
Florence M G
FM
Cavalli
Richard
R
Bourgon
Wolfgang
W
Huber
Juan M
JM
Vaquerizas
Nicholas M
NM
Luscombe
D000465:Algorithms; D019295:Computational Biology; D030541:Databases, Genetic; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods*; D005796:Genes; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012372:ROC Curve; D012680:Sensitivity and Specificity; D012984:Software