Detecting microRNA binding and siRNA off-target effects from expression data

Sylamer is a method for detecting microRNA target and small interfering (si)RNA off-target signals from expression data. The input is a ranked genelist from up to downregulated 3′ untranslated regions (UTRs) following an miRNA or RNAi experiment. The output is a landscape plot that tracks occurrence...

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Detalles Bibliográficos
Autores principales: van Dongen, Stijn, Abreu-Goodger, Cei, Enright, Anton J
Formato: Texto
Lenguaje:English
Publicado: 2008
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2635553/
https://www.ncbi.nlm.nih.gov/pubmed/18978784
http://dx.doi.org/10.1038/nmeth.1267
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author van Dongen, Stijn
Abreu-Goodger, Cei
Enright, Anton J
author_facet van Dongen, Stijn
Abreu-Goodger, Cei
Enright, Anton J
author_sort van Dongen, Stijn
collection PubMed
description Sylamer is a method for detecting microRNA target and small interfering (si)RNA off-target signals from expression data. The input is a ranked genelist from up to downregulated 3′ untranslated regions (UTRs) following an miRNA or RNAi experiment. The output is a landscape plot that tracks occurrence biases using hypergeometric P-values for all words across the gene ranking. The utility, speed, and accuracy of the approach on several miRNA and siRNA datasets are demonstrated.
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spelling pubmed-26355532009-06-01 Detecting microRNA binding and siRNA off-target effects from expression data van Dongen, Stijn Abreu-Goodger, Cei Enright, Anton J Nat Methods Article Sylamer is a method for detecting microRNA target and small interfering (si)RNA off-target signals from expression data. The input is a ranked genelist from up to downregulated 3′ untranslated regions (UTRs) following an miRNA or RNAi experiment. The output is a landscape plot that tracks occurrence biases using hypergeometric P-values for all words across the gene ranking. The utility, speed, and accuracy of the approach on several miRNA and siRNA datasets are demonstrated. 2008-11-02 2008-12 /pmc/articles/PMC2635553/ /pubmed/18978784 http://dx.doi.org/10.1038/nmeth.1267 Text en
spellingShingle Article
van Dongen, Stijn
Abreu-Goodger, Cei
Enright, Anton J
Detecting microRNA binding and siRNA off-target effects from expression data
title Detecting microRNA binding and siRNA off-target effects from expression data
title_full Detecting microRNA binding and siRNA off-target effects from expression data
title_fullStr Detecting microRNA binding and siRNA off-target effects from expression data
title_full_unstemmed Detecting microRNA binding and siRNA off-target effects from expression data
title_short Detecting microRNA binding and siRNA off-target effects from expression data
title_sort detecting microrna binding and sirna off-target effects from expression data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2635553/
https://www.ncbi.nlm.nih.gov/pubmed/18978784
http://dx.doi.org/10.1038/nmeth.1267
work_keys_str_mv AT vandongenstijn detectingmicrornabindingandsirnaofftargeteffectsfromexpressiondata
AT abreugoodgercei detectingmicrornabindingandsirnaofftargeteffectsfromexpressiondata
AT enrightantonj detectingmicrornabindingandsirnaofftargeteffectsfromexpressiondata

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