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About siDRM

    siDRM is an implementation of the DRM rule sets for selecting effective siRNAs. These rule sets were obtained in the following three steps: (1) A survey of significant features was conducted on the large and diverse dataset compiled from siRecords, with all known features implicated to have impacts on the siRNA efficacy. This survey resulted in a list of features associated with a significant up-shift of the siRNA efficacy distribution, and/or significantly boosting the chances of achieving higher siRNA efficacy. (2) A feature combination analysis was performed to exploit the positive cooperativity of the significant features identified in their joint effects in boosting the siRNA efficacy. A list of feature combinations (also called rules) leading to substantial improvement in efficacy in the training dataset was obtained. (3) The DRM (or disjunctive rule merging) algorithm was applied to merge and reorganize the rules obtained, resulting in a bundle of rule sets (or disjunctions of rules), ordered descendingly in stringency.

 
 
 
References
  • Gong W, Ren Y, Xu Q, Wang Y, Lin D, Zhou H, Li T: Integrated siRNA design based on surveying of features associated with high RNAi effectiveness. BMC Bioinformatics 2006, 7: 516. . [PubMed] [Full-text]
  • Ren Y, Gong W, Xu Q, Zheng X, Lin D, Wang Y, Li T: siRecords: an extensive database of mammalian siRNAs with efficacy ratings. Bioinformatics 2006, 22: 1027-1028. [PubMed]
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