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PMID: 18978784 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nature methods ·Vol. 5 ·No. 12 ·2008-12-00 ·Pages 1023-5

van Dongen S, Abreu-Goodger C, Enright AJ

Abstract

Sylamer 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.

MeSH Terms

Algorithms Gene Expression Profiling/methods Gene Targeting/methods MicroRNAs/genetics RNA, Small Interfering/genetics Sequence Analysis, DNA/methods Software

Chemicals

MicroRNAs RNA, Small Interfering

Authors & Affiliations

3 authors, click to expand affiliations / ORCID

van Dongen Stijn

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Abreu-Goodger Cei

Enright Anton J

References (15)

15 references, click to expand

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Article Info

Journal

Nature methods

Abbr.

Nat Methods

ISSN

1548-7105

DOI

10.1038/nmeth.1267

Published

2008-12-00

Epub

2008-00-02

Pages

1023-5

Language

English

Region

United States

NLM ID

101215604

PMCID

PMC2635553

Subset

Grants

Wellcome Trust · 077040 · United Kingdom

External Links

PubMed source DOI: 10.1038/nmeth.1267 PMC Full Text View journal details

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