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

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.

Keywords

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

Journal Title

Nat Methods

Journal ISSN

1548-7091
1548-7105

Volume Title

5

Publisher

Springer Nature

Publisher DOI

https://doi.org/10.1038/nmeth.1267

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Collections

Scholarly Works - Pathology