Detecting microRNA binding and siRNA off-target effects from expression data
By Stijn van Dongen, Cei Abreu-Goodger, Anton J. Enright. Nature Methods, 2008
296 citations recorded by the source corpus.
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.
Subfields: Cancer Research, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/3b1c72c5d839289425b82a47c4f174ead70aee74
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Citations in the corpus
- Essential metabolic, anti-inflammatory, and anti-tumorigenic functions of miR-122 in liver. (2012, unknown): “(A) Sylamer plots (17) showing the enriched hexamers (top), heptamers (middle), and octamers (bottom) in transcripts that are upregulated in LKO livers.”
- MicroRNA-155 modulates the interleukin-1 signaling pathway in activated human monocyte-derived dendritic cells (2009, methodology): “We validated our experimental approach using the Sylamer software (21) and demonstrated that miR-155 inhibition in activated DCs, clearly leads to the favored up-regulation of mRNAs containing miR-155 seeds (6 and 7 nt) in their 3 UTR, but not the seeds of anti-miR155-LNA or of the scramble-LNA olig”
- siRNA vs. shRNA: similarities and differences. (2009, methodology): “Methods for microarray-based off-target screening are reviewed in detail elsewhere [169,170].”
- In vivo delivery of miRNAs for cancer therapy: Challenges and strategies (2014, background): “The combination strategy can be added into the miRNA therapy to avoid unintended off-target effects [81].”
- An overview of microRNAs (2015, background): “This can be done by microarray profiling and several analysis tools are available[112-115].”