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.
van Dongen
Stijn
S
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
Abreu-Goodger
Cei
C
Enright
Anton J
AJ
D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D018390:Gene Targeting / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D035683:MicroRNAs; D034741:RNA, Small Interfering