Mercurial > repos > mkim8 > mintest
annotate offtarget/README.md @ 0:94332d4947cb draft default tip
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| author | mkim8 |
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| date | Thu, 13 Mar 2014 19:43:26 -0400 |
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| 0 | 1 offtarget |
| 2 ========= | |
| 3 | |
| 4 DecoRNAi | |
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| 6 High-throughput RNAi screening has been widely used in a spectrum of biomedical research and made it possible to study functional genomics. However, a challenge for authentic biological interpretation of large-scale siRNA or shRNA-mediated loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA and shRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling that can result from short regions (~6 nucleotides) of oligonucleotide complementarity to many different mRNAs. To help identify and correct miRNA-mimic off-target effects, we have developed DecoRNAi (deconvolution analysis of RNAi screening data) for automated quantitation and annotation of microRNA-like off-target effects in primary RNAi screening data sets. DecoRNAi can effectively identify and correct off-target effects from primary screening data and provide data visualization for study and publication. DecoRNAi contains pre-computed seed sequence families for 3 commonly employed commercial siRNA libraries. For custom collections, the tool will compute seed sequence membership from a user-supplied reagent sequence table. All parameters are tunable and output files include global data visualization, the identified seed family associations, the siRNA pools containing off-target seed families, corrected z-scores and the potential miRNAs with phenotypes of interest. | |
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| 8 Author Rui Zhong. For any suggestions or inquiries please contact rui.zhong@utsouthwestern.edu | |
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