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Open Access Highly Accessed Software

ScreenSifter: analysis and visualization of RNAi screening data

Pankaj Kumar1, Germaine Goh1, Sarawut Wongphayak1, Dimitri Moreau1 and Frédéric Bard12*

Author Affiliations

1 Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos 138673, Singapore

2 Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore

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BMC Bioinformatics 2013, 14:290  doi:10.1186/1471-2105-14-290

Published: 3 October 2013

Abstract

Background

RNAi screening is a powerful method to study the genetics of intracellular processes in metazoans. Technically, the approach has been largely inspired by techniques and tools developed for compound screening, including those for data analysis. However, by contrast with compounds, RNAi inducing agents can be linked to a large body of gene-centric, publically available data. However, the currently available software applications to analyze RNAi screen data usually lack the ability to visualize associated gene information in an interactive fashion.

Results

Here, we present ScreenSifter, an open-source desktop application developed to facilitate storing, statistical analysis and rapid and intuitive biological data mining of RNAi screening datasets. The interface facilitates meta-data acquisition and long-term safe-storage, while the graphical user interface helps the definition of a hit list and the visualization of biological modules among the hits, through Gene Ontology and protein-protein interaction analyses. The application also allows the visualization of screen-to-screen comparisons.

Conclusions

Our software package, ScreenSifter, can accelerate and facilitate screen data analysis and enable discovery by providing unique biological data visualization capabilities.

Keywords:
RNAi screening; Data visualization; Database; Data analysis; Data mining