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

by: Stijn van Dongen, Cei Abreu-Goodger, Anton J. Enright

Nature methods, Vol. 5, No. 12. (2 December 2008), pp. 1023-1025.

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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.

@article{dongen08, 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.}, author = {van Dongen, Stijn and Abreu-Goodger, Cei and Enright, Anton J.}, citeulike-article-id = {3478108}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nmeth.1267}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nmeth.1267}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18978784}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18978784}, day = {2}, doi = {10.1038/nmeth.1267}, issn = {1548-7105}, journal = {Nature methods}, keywords = {microrna, microrna\_mrna, sirna, sylamer}, month = {December}, number = {12}, pages = {1023--1025}, posted-at = {2009-11-05 11:57:08}, priority = {2}, publisher = {Nature Publishing Group}, title = {Detecting microRNA binding and siRNA off-target effects from expression data.}, url = {http://dx.doi.org/10.1038/nmeth.1267}, volume = {5}, year = {2008} }

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TY - JOUR ID - dongen08 L3 - citeulike-article-id:3478108 N2 - 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. IS - 12 JF - Nature methods SN - 1548-7105 EP - 1025 TI - Detecting microRNA binding and siRNA off-target effects from expression data. PB - Nature Publishing Group VL - 5 SP - 1023 KW - microrna KW - microrna_mrna KW - sirna KW - sylamer AU - van Dongen, Stijn AU - Abreu-Goodger, Cei AU - Enright, Anton PY - 2008/12/02/ UR - http://dx.doi.org/10.1038/nmeth.1267 ER -

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

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