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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

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


  • MicroRNAs
  • RNA, Small Interfering