{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T13:03:24Z","timestamp":1762866204872},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: High-throughput cell-based phenotypic screening has become an increasingly important technology for discovering new drug targets and assigning gene functions. Such experiments use hundreds of 96-well or 384-well plates, to cover whole-genome RNAi collections and\/or chemical compound files, and often collect measurements that are sensitive to spatial background noise whose patterns can vary across individual plates. Correcting these position effects can substantially improve measurement accuracy and screening success.<\/jats:p>\n               <jats:p>Result: We developed SbacHTS (Spatial background noise correction for High-Throughput RNAi Screening) software for visualization, estimation and correction of spatial background noise in high-throughput RNAi screens. SbacHTS is supported on the Galaxy open-source framework with a user-friendly open access web interface. We find that SbacHTS software can effectively detect and correct spatial background noise, increase signal to noise ratio and enhance statistical detection power in high-throughput RNAi screening experiments.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.galaxy.qbrc.org\/<\/jats:p>\n               <jats:p>Contact: \u00a0Guanghua.Xiao@UTSouthwestern.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt358","type":"journal-article","created":{"date-parts":[[2013,6,29]],"date-time":"2013-06-29T04:15:06Z","timestamp":1372479306000},"page":"2218-2220","source":"Crossref","is-referenced-by-count":2,"title":["SbacHTS: Spatial background noise correction for High-Throughput RNAi Screening"],"prefix":"10.1093","volume":"29","author":[{"given":"Rui","family":"Zhong","sequence":"first","affiliation":[{"name":"1 Quantitative Biomedical Research Center, Department of Clinical Science, 2Harold C. Simmons Comprehensive Cancer Center and 3Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA"}]},{"given":"Min Soo","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Quantitative Biomedical Research Center, Department of Clinical Science, 2Harold C. Simmons Comprehensive Cancer Center and 3Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA"}]},{"given":"Michael A.","family":"White","sequence":"additional","affiliation":[{"name":"1 Quantitative Biomedical Research Center, Department of Clinical Science, 2Harold C. Simmons Comprehensive Cancer Center and 3Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA"},{"name":"1 Quantitative Biomedical Research Center, Department of Clinical Science, 2Harold C. Simmons Comprehensive Cancer Center and 3Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA"}]},{"given":"Yang","family":"Xie","sequence":"additional","affiliation":[{"name":"1 Quantitative Biomedical Research Center, Department of Clinical Science, 2Harold C. Simmons Comprehensive Cancer Center and 3Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA"},{"name":"1 Quantitative Biomedical Research Center, Department of Clinical Science, 2Harold C. Simmons Comprehensive Cancer Center and 3Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA"}]},{"given":"Guanghua","family":"Xiao","sequence":"additional","affiliation":[{"name":"1 Quantitative Biomedical Research Center, Department of Clinical Science, 2Harold C. Simmons Comprehensive Cancer Center and 3Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA"}]}],"member":"286","published-online":{"date-parts":[[2013,6,28]]},"reference":[{"key":"2023012810462825500_btt358-B1","doi-asserted-by":"crossref","DOI":"10.1201\/9780203487808","volume-title":"Hierarchical Modeling and Analysis for Spatial Data","author":"Banerjee","year":"2003"},{"key":"2023012810462825500_btt358-B2","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1038\/nmeth.1351","article-title":"Statistical methods for analysis of high-throughput RNA interference screens","volume":"6","author":"Birmingham","year":"2009","journal-title":"Nat. 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Biotechnol."},{"key":"2023012810462825500_btt358-B7","doi-asserted-by":"crossref","first-page":"1945","DOI":"10.1093\/bioinformatics\/bts288","article-title":"HCS-Analyzer: open source software for high-content screening data correction and analysis","volume":"28","author":"Ogier","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810462825500_btt358-B8","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/nature10546","article-title":"Image-based genome-wide siRNA screen identifies selective autophagy factors","volume":"480","author":"Orvedahl","year":"2011","journal-title":"Nature"},{"key":"2023012810462825500_btt358-B9","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.1093\/bioinformatics\/btg148","article-title":"Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values","volume":"19","author":"Pounds","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012810462825500_btt358-B10","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1038\/nature05697","article-title":"Synthetic lethal screen identification of chemosensitizer loci in cancer cells","volume":"446","author":"Whitehurst","year":"2007","journal-title":"Nature"},{"key":"2023012810462825500_btt358-B11","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1093\/bioinformatics\/btt060","article-title":"displayHTS: a R package for displaying data and results from high-throughput screening experiments","volume":"29","author":"Zhang","year":"2013","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/17\/2218\/48890740\/bioinformatics_29_17_2218.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/17\/2218\/48890740\/bioinformatics_29_17_2218.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:33:52Z","timestamp":1674909232000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/17\/2218\/241740"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,6,28]]},"references-count":11,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2013,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt358","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,9,1]]},"published":{"date-parts":[[2013,6,28]]}}}