ScreenSifter: analysis and visualization of RNAi screening data

BMC Bioinformatics

Pankaj Kumar²  Germaine Goh²  Sarawut Wongphayak²  Dimitri Moreau²  Frédéric Bard¹ 

[1] Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore

[2] Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos 138673, Singapore

关键词: Data mining;    Data analysis;    Database;    Data visualization;    RNAi screening;   

Others  :  1087746
DOI  :  10.1186/1471-2105-14-290

 received in 2013-06-10, accepted in 2013-09-27,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Kumar et al.; licensee BioMed Central Ltd.

【 图 表 】

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