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Nat Commun. 2016 Feb 23;7:10578. doi: 10.1038/ncomms10578.

An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.

Author information

1
Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
2
Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.
3
ICCB-Longwood Screening Facility, Harvard Medical School, Boston, Massachusetts 02115, USA.
4
Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3002, Australia.
5
Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA.

Abstract

RNAi screens are widely used in functional genomics. Although the screen data can be susceptible to a number of experimental biases, many of these can be corrected by computational analysis. For this purpose, here we have developed a web-based platform for integrated analysis and visualization of RNAi screen data named CARD (for Comprehensive Analysis of RNAi Data; available at https://card.niaid.nih.gov). CARD allows the user to seamlessly carry out sequential steps in a rigorous data analysis workflow, including normalization, off-target analysis, integration of gene expression data, optimal thresholds for hit selection and network/pathway analysis. To evaluate the utility of CARD, we describe analysis of three genome-scale siRNA screens and demonstrate: (i) a significant increase both in selection of subsequently validated hits and in rejection of false positives, (ii) an increased overlap of hits from independent screens of the same biology and (iii) insight to microRNA (miRNA) activity based on siRNA seed enrichment.

PMID:
26902267
DOI:
10.1038/ncomms10578
[Indexed for MEDLINE]
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