title: An interactive web-based application for Comprehensive Analysis of RNAi-screen Data.
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.
authors.affiliation: Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Bhaskar
authors.initials: B
authors.lastname: Dutta
authors.affiliation: Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Alaleh
authors.initials: A
authors.lastname: Azhir
authors.affiliation: Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Louis-Henri
authors.initials: LH
authors.lastname: Merino
authors.affiliation: Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Yongjian
authors.initials: Y
authors.lastname: Guo
authors.affiliation: Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Swetha
authors.initials: S
authors.lastname: Revanur
authors.affiliation: Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.
authors.forename: Piyush B
authors.initials: PB
authors.lastname: Madhamshettiwar
authors.affiliation: Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Ronald N
authors.initials: RN
authors.lastname: Germain
authors.affiliation: ICCB-Longwood Screening Facility, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Jennifer A
authors.initials: JA
authors.lastname: Smith
authors.affiliation: Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.|Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3002, Australia.
authors.forename: Kaylene J
authors.initials: KJ
authors.lastname: Simpson
authors.affiliation: Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Martin
authors.affiliation: Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Eugen
authors.initials: E
authors.lastname: Buehler
authors.affiliation: Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Eugen
authors.initials: E
authors.lastname: Beuhler
authors.affiliation: Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Iain D C
authors.initials: ID
authors.lastname: Fraser
mesh_terms: D023281:Genomics; D034622:RNA Interference; D012984:Software