{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,3]],"date-time":"2024-08-03T21:43:52Z","timestamp":1722721432907},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Accurate estimation of DNA copy numbers from array comparative genomic hybridization (CGH) data is important for characterizing the cancer genome. An important part of this process is the segmentation of the log-ratios between the sample and control DNA along the chromosome into regions of different copy numbers. However, multiple algorithms are available in the literature for this procedure and the results can vary substantially among these. Thus, a visualization tool that can display the segmented profiles from a number of methods can be helpful to the biologist or the clinician to ascertain that a feature of interest did not arise as an artifact of the algorithm. Such a tool also allows the methodologist to easily contrast his method against others.<\/jats:p>\n               <jats:p>We developed a web-based tool that applies a number of popular algorithms to a single array CGH profile entered by the user. It generates a heatmap panel of the segmented profiles for each method as well as a consensus profile. The clickable heatmap can be moved along the chromosome and zoomed in or out. It also displays the time that each algorithm took and provides numerical values of the segmented profiles for download. The web interface calls algorithms written in the statistical language R. We encourage developers of new algorithms to submit their routines to be incorporated into the website.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/compbio.med.harvard.edu\/CGHweb<\/jats:p>\n               <jats:p>Contact: \u00a0peter_park@harvard.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn067","type":"journal-article","created":{"date-parts":[[2008,2,23]],"date-time":"2008-02-23T01:34:37Z","timestamp":1203730477000},"page":"1014-1015","source":"Crossref","is-referenced-by-count":40,"title":["CGHweb: a tool for comparing DNA copy number segmentations from multiple algorithms"],"prefix":"10.1093","volume":"24","author":[{"given":"Weil","family":"Lai","sequence":"first","affiliation":[{"name":"1 Harvard-Partners Center for Genetics and Genomics and 2Informatics Program, Children's Hospital, Boston, MA 02139, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vidhu","family":"Choudhary","sequence":"additional","affiliation":[{"name":"1 Harvard-Partners Center for Genetics and Genomics and 2Informatics Program, Children's Hospital, Boston, MA 02139, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter J.","family":"Park","sequence":"additional","affiliation":[{"name":"1 Harvard-Partners Center for Genetics and Genomics and 2Informatics Program, Children's Hospital, Boston, MA 02139, USA"},{"name":"1 Harvard-Partners Center for Genetics and Genomics and 2Informatics Program, Children's Hospital, Boston, MA 02139, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,2,22]]},"reference":[{"key":"2023020209532566900_B1","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1093\/bioinformatics\/btg230","article-title":"CGH-Plotter: MATLAB toolbox for CGH-data analysis","volume":"19","author":"Autio","year":"2003","journal-title":"Bioinformatics"},{"key":"2023020209532566900_B2","doi-asserted-by":"crossref","first-page":"20007","DOI":"10.1073\/pnas.0710052104","article-title":"Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma","volume":"104","author":"Beroukhim","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023020209532566900_B3","doi-asserted-by":"crossref","first-page":"1540","DOI":"10.1093\/bioinformatics\/18.11.1540","article-title":"SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis","volume":"18","author":"Colantuoni","year":"2002","journal-title":"Bioinformatics"},{"issue":"Web Server issue","key":"2023020209532566900_B4","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1093\/nar\/gkm257","article-title":"ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling","volume":"35","author":"Conde","year":"2007","journal-title":"Nucleic Acids Res"},{"issue":"Web Server issue","key":"2023020209532566900_B5","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1093\/nar\/gkm229","article-title":"Asterias: integrated analysis of expression and a CGH data using an open-source, web-based, parallelized software suite","volume":"35","author":"Diaz-Uriarte","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023020209532566900_B6","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1101\/gr.5076506","article-title":"STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments","volume":"16","author":"Diskin","year":"2006","journal-title":"Genome Res"},{"key":"2023020209532566900_B7","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1093\/biostatistics\/kxj015","article-title":"A pseudolikelihood approach for simultaneous analysis of array comparative genomic hybridizations","volume":"7","author":"Engler","year":"2006","journal-title":"Biostatistics"},{"key":"2023020209532566900_B8","doi-asserted-by":"crossref","first-page":"3763","DOI":"10.1093\/bioinformatics\/bti611","article-title":"Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data","volume":"21","author":"Lai","year":"2005","journal-title":"Bioinformatics"},{"issue":"Web Server issue","key":"2023020209532566900_B9","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1093\/nar\/gkl215","article-title":"CAPweb: a bioinformatics CGH array Analysis Platform","volume":"34","author":"Liva","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023020209532566900_B10","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1093\/biostatistics\/kxh008","article-title":"Circular binary segmentation for the analysis of array-based DNA copy number data","volume":"5","author":"Olshen","year":"2004","journal-title":"Biostatistics"},{"key":"2023020209532566900_B11","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/2524","article-title":"High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays","volume":"20","author":"Pinkel","year":"1998","journal-title":"Nat. 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