Brief Communication abstract
Nature Methods 5, 1023 - 1025 (2008)
Published online: 2 November 2008 | doi:10.1038/nmeth.1267
Detecting microRNA binding and siRNA off-target effects from expression data
Stijn van Dongen1,2,3, Cei Abreu-Goodger1,3 & Anton J Enright1,2
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Top of pageSylamer is a method for detecting microRNA target and small interfering RNA off-target signals in 3' untranslated regions from a ranked gene list, sorted from upregulated to downregulated, after a microRNA perturbation or RNA interference experiment. The output is a landscape plot that tracks occurrence biases using hypergeometric P-values for all words across the gene ranking. We demonstrated the utility, speed and accuracy of this approach on several datasets.
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
- Present address: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
- These authors contributed equally to this work.
Correspondence to: Anton J Enright1,2 e-mail: aje@ebi.ac.uk
