{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T22:45:55Z","timestamp":1778107555754,"version":"3.51.4"},"reference-count":19,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The analysis of high-throughput screening data sets is an expanding field in bioinformatics. High-throughput screens by RNAi generate large primary data sets which need to be analyzed and annotated to identify relevant phenotypic hits. Large-scale RNAi screens are frequently used to identify novel factors that influence a broad range of cellular processes, including signaling pathway activity, cell proliferation, and host cell infection. Here, we present a web-based application utility for the end-to-end analysis of large cell-based screening experiments by cellHTS2.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The software guides the user through the configuration steps that are required for the analysis of single or multi-channel experiments. The web-application provides options for various standardization and normalization methods, annotation of data sets and a comprehensive HTML report of the screening data analysis, including a ranked hit list. Sessions can be saved and restored for later re-analysis. The web frontend for the cellHTS2 R\/Bioconductor package interacts with it through an R-server implementation that enables highly parallel analysis of screening data sets. web cellHTS2 further provides a file import and configuration module for common file formats.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The implemented web-application facilitates the analysis of high-throughput data sets and provides a user-friendly interface. web cellHTS2 is accessible online at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/web-cellHTS2.dkfz.de\" ext-link-type=\"uri\">http:\/\/web-cellHTS2.dkfz.de<\/jats:ext-link>. A standalone version as a virtual appliance and source code for platforms supporting Java 1.5.0 can be downloaded from the web cellHTS2 page. web cellHTS2 is freely distributed under GPL.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-185","type":"journal-article","created":{"date-parts":[[2010,5,4]],"date-time":"2010-05-04T19:56:04Z","timestamp":1273002964000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":58,"title":["web cellHTS2: A web-application for the analysis of high-throughput screening data"],"prefix":"10.1186","volume":"11","author":[{"given":"Oliver","family":"Pelz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Moritz","family":"Gilsdorf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Boutros","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,4,12]]},"reference":[{"key":"3642_CR1","doi-asserted-by":"publisher","first-page":"554","DOI":"10.1038\/nrg2364","volume":"9","author":"M Boutros","year":"2008","unstructured":"Boutros M, Ahringer J: The art and design of genetic screens: RNA interference. Nature Reviews Genetics 2008, 9: 554\u2013566. 10.1038\/nrg2364","journal-title":"Nature Reviews Genetics"},{"key":"3642_CR2","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/nrm1860","volume":"7","author":"J Moffat","year":"2006","unstructured":"Moffat J, Sabatini DM: Building mammalian signalling pathways with RNAi screens. Nature Reviews Molecular Cell Biology 2006, 7: 177\u2013187. 10.1038\/nrm1860","journal-title":"Nature Reviews Molecular Cell Biology"},{"key":"3642_CR3","doi-asserted-by":"publisher","first-page":"D489","DOI":"10.1093\/nar\/gkj114","volume":"34","author":"I Flockhart","year":"2006","unstructured":"Flockhart I, Booker M, Kiger A, Boutros M, Armknecht S, Ramadan N, Richardson K, Xu A, Perrimon N, Mathey-Prevot B: FlyRNAi: the Drosophila RNAi screening center database. Nucleic Acids Research 2006, 34: D489\u2013494. 10.1093\/nar\/gkj114","journal-title":"Nucleic Acids Research"},{"key":"3642_CR4","doi-asserted-by":"publisher","first-page":"523","DOI":"10.1016\/j.cell.2006.04.009","volume":"125","author":"K Bartscherer","year":"2006","unstructured":"Bartscherer K, Pelte N, Ingelfinger D, Boutros M: Secretion of Wnt ligands requires Evi, aconserved transmembrane protein. Cell 2006, 125: 523\u2013533. 10.1016\/j.cell.2006.04.009","journal-title":"Cell"},{"key":"3642_CR5","doi-asserted-by":"publisher","first-page":"604","DOI":"10.1038\/nature04377","volume":"439","author":"F Bard","year":"2006","unstructured":"Bard F, Casano L, Mallabiabarrena A, Wallace E, Saito K, Kitayama H, Guizzunti G, Hu Y, Wendler F, Dasgupta R, Perrimon N, Malhotra V: Functional genomics reveals genes involvedin protein secretion and Golgi organization. Nature 2006, 439: 604\u2013607. 10.1038\/nature04377","journal-title":"Nature"},{"key":"3642_CR6","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1016\/j.ccr.2009.02.023","volume":"15","author":"S Huang","year":"2009","unstructured":"Huang S, Laoukili J, Epping MT, Koster J, H\u00f6lzel M, Westerman BA, Nijkamp W, Hata A, Asgharzadeh S, Seeger RC, Versteeg R, Beijersbergen RL, Bernards R: ZNF423 is criticallyrequired for retinoic acid-induced differentiation and is a marker of neuroblastoma outcome. Cancer Cell 2009, 15: 328\u2013340. 10.1016\/j.ccr.2009.02.023","journal-title":"Cancer Cell"},{"key":"3642_CR7","doi-asserted-by":"publisher","first-page":"R66","DOI":"10.1186\/gb-2006-7-7-r66","volume":"7","author":"M Boutros","year":"2006","unstructured":"Boutros M, Bras LP, Huber W: Analysis of cell-based RNAi screens. Genome Biology 2006, 7: R66. 10.1186\/gb-2006-7-7-r66","journal-title":"Genome Biology"},{"key":"3642_CR8","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1038\/nmeth.1351","volume":"6","author":"A Birmingham","year":"2009","unstructured":"Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, Santoyo-Lopez J, Dunican DJ, Long A, Kelleher D, Smith Q, Beijersbergen RL, Ghazal P, Shamu CE: Statistical methods for analysis of high-throughput RNA interference screens. Nature Methods 2009, 6: 569\u201375. 10.1038\/nmeth.1351","journal-title":"Nature Methods"},{"key":"3642_CR9","doi-asserted-by":"publisher","first-page":"678","DOI":"10.1093\/bioinformatics\/btp014","volume":"25","author":"N Rieber","year":"2009","unstructured":"Rieber N, Knapp B, Eils R, Kaderali L: RNAither, an automated pipeline for the statisticalanalysis of high-throughput RNAi screens. Bioinformatics 2009, 25: 678\u20139. 10.1093\/bioinformatics\/btp014","journal-title":"Bioinformatics"},{"key":"3642_CR10","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1177\/1087057107312035","volume":"13","author":"N Chung","year":"2008","unstructured":"Chung N, Zhang XD, Kreamer A, Locco L, Kuan PF, Bartz S, Linsley PS, Ferrer M, Strulovici B: Median absolute deviation to improve hit selection for genome-scale RNAi screens. Journal of Biomolecular Screening 2008, 13: 149\u201358. 10.1177\/1087057107312035","journal-title":"Journal of Biomolecular Screening"},{"key":"3642_CR11","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1177\/108705719900400206","volume":"4","author":"JH Zhang","year":"1999","unstructured":"Zhang JH, Chung TD, Oldenburg KR: A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays. Journal of Biomolecular Screening 1999, 4: 67\u201373. 10.1177\/108705719900400206","journal-title":"Journal of Biomolecular Screening"},{"key":"3642_CR12","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J: Bioconductor: opensoftware development for computational biology and bioinformatics. Genome Biology 2004, 5: R80. 10.1186\/gb-2004-5-10-r80","journal-title":"Genome Biology"},{"key":"3642_CR13","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1038\/nbt1186","volume":"24","author":"N Malo","year":"2006","unstructured":"Malo N, Hanley JA, Cerquozzi S, Pelletier J, Nadon R: Statistical practice in high-throughput screening data analysis. Nature Biotechnology 2006, 24: 167\u201375. 10.1038\/nbt1186","journal-title":"Nature Biotechnology"},{"key":"3642_CR14","unstructured":"Apache Tapestry 5[http:\/\/tapestry.apache.org]"},{"key":"3642_CR15","unstructured":"Apache Tomcat 5.5[http:\/\/tomcat.apache.org]"},{"key":"3642_CR16","unstructured":"Jetty Java webserver[http:\/\/www.mortbay.org\/jetty\/]"},{"key":"3642_CR17","unstructured":"Virtual Box[http:\/\/www.virtualbox.org\/]"},{"key":"3642_CR18","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1177\/1087057103258285","volume":"8","author":"C Brideau","year":"2003","unstructured":"Brideau C, Gunter B, Pikounis B, Liaw A: Improved statistical methods for hit selection inhigh-throughput screening. Journal of Biomolecular Screening 2003, 8: 634\u2013647. 10.1177\/1087057103258285","journal-title":"Journal of Biomolecular Screening"},{"key":"3642_CR19","doi-asserted-by":"publisher","first-page":"D492","DOI":"10.1093\/nar\/gkl906","volume":"35","author":"T Horn","year":"2007","unstructured":"Horn T, Arziman Z, Berger J, Boutros M: GenomeRNAi: a database for cell-based RNAiphenotypes. Nucleic Acids Research 2007, 35: D492\u20137. 10.1093\/nar\/gkl906","journal-title":"Nucleic Acids Research"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-185.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T12:14:44Z","timestamp":1630498484000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-185"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,12]]},"references-count":19,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3642"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-185","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,4,12]]},"assertion":[{"value":"3 October 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 April 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 April 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"185"}}