Reconsideration of in-silico siRNA design based on feature selection: A cross-platform data integration perspective

Qi Liu, Han Zhou, Juan Cui, Zhiwei Cao, Ying Xu

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


RNA interference via exogenous short interference RNAs (siRNA) is increasingly more widely employed as a tool in gene function studies, drug target discovery and disease treatment. Currently there is a strong need for rational siRNA design to achieve more reliable and specific gene silencing; and to keep up with the increasing needs for a wider range of applications. While progress has been made in the ability to design siRNAs with specific targets, we are clearly at an infancy stage towards achieving rational design of siRNAs with high efficacy. Among the many obstacles to overcome, lack of general understanding of what sequence features of siRNAs may affect their silencing efficacy and of large-scale homogeneous data needed to carry out such association analyses represents two challenges. To address these issues, we investigated a feature-selection based in-silico siRNA design from a novel cross-platform data integration perspective. An integration analysis of 4,482 siRNAs from ten meta-datasets was conducted for ranking siRNA features, according to their possible importance to the silencing efficacy of siRNAs across heterogeneous data sources. Our ranking analysis revealed for the first time the most relevant features based on cross-platform experiments, which compares favorably with the traditional in-silico siRNA feature screening based on the small samples of individual platform data. We believe that our feature ranking analysis can offer more creditable suggestions to help improving the design of siRNA with specific silencing targets. Data and scripts are available at

Original languageEnglish (US)
Article numbere37879
JournalPloS one
Issue number5
StatePublished - May 24 2012
Externally publishedYes

ASJC Scopus subject areas

  • General


Dive into the research topics of 'Reconsideration of in-silico siRNA design based on feature selection: A cross-platform data integration perspective'. Together they form a unique fingerprint.

Cite this