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Nat Methods. 2008 Dec;5(12):1023-5. doi: 10.1038/nmeth.1267. Epub 2008 Nov 2.

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

Author information

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

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.

PMID:
18978784
PMCID:
PMC2635553
DOI:
10.1038/nmeth.1267
[Indexed for MEDLINE]
Free PMC Article

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