title: iScreen: Image-Based High-Content RNAi Screening Analysis Tools.
abstract: High-throughput RNA interference (RNAi) screening has opened up a path to investigating functional genomics in a genome-wide pattern. However, such studies are often restricted to assays that have a single readout format. Recently, advanced image technologies have been coupled with high-throughput RNAi screening to develop high-content screening, in which one or more cell image(s), instead of a single readout, were generated from each well. This image-based high-content screening technology has led to genome-wide functional annotation in a wider spectrum of biological research studies, as well as in drug and target discovery, so that complex cellular phenotypes can be measured in a multiparametric format. Despite these advances, data analysis and visualization tools are still largely lacking for these types of experiments. Therefore, we developed iScreen (image-Based High-content RNAi Screening Analysis Tool), an R package for the statistical modeling and visualization of image-based high-content RNAi screening. Two case studies were used to demonstrate the capability and efficiency of the iScreen package. iScreen is available for download on CRAN (http://cran.cnr.berkeley.edu/web/packages/iScreen/index.html). The user manual is also available as a supplementary document.
authors.affiliation: Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: Rui
authors.initials: R
authors.lastname: Zhong
authors.affiliation: Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: Xiaonan
authors.initials: X
authors.lastname: Dong
authors.affiliation: Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA Center for Autophagy Research, University of Texas Southwestern Medical Center, Dallas, TX, USA Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: Beth
authors.initials: B
authors.lastname: Levine
authors.affiliation: Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.affiliation: Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA guanghua.xiao@utsouthwestern.edu.
authors.forename: Guanghua
authors.initials: G
authors.lastname: Xiao
mesh_terms: D001343:Autophagy / Q000235:genetics; D023281:Genomics / Q000379:methods; D006367:HeLa Cells; D057166:High-Throughput Screening Assays; D006801:Humans; D057054:Molecular Imaging / Q000379:methods*; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D034741:RNA, Small Interfering
keywords: RNA interference; RNAi; genomics; high-content screening; shRNA; statistical analyses