{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T01:33:59Z","timestamp":1722389639925},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2007,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: DNA copy number aberrations are frequently found in different types of cancer. Recent developments of microarray-based approaches have broadened the knowledge on number and structure of such aberrations. High-density single nucleotide polymorphism (SNP) microarrays provide an extremely high resolution with up to 500\u2009000 SNPs per genome. Owing to the enormous amount of data the detection of common aberrations in large datasets is a great challenge. We describe a novel open source software tool\u2014IdeogramBrowser\u2014which was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards. Visualization of consensus regions together with gene representation allows the explorative assessment of the data.<\/jats:p><jats:p>Availability: IdeogramBrowser and its source code are freely available under a creative commons license and can be obtained from .\u2009\u2009IdeogramBrowser\u2009is a platform independent Java application.<\/jats:p><jats:p>Contact: \u00a0hans.kestler@uni-ulm.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl608","type":"journal-article","created":{"date-parts":[[2006,12,1]],"date-time":"2006-12-01T01:24:12Z","timestamp":1164936252000},"page":"496-497","source":"Crossref","is-referenced-by-count":21,"title":["Visualization of genomic aberrations using Affymetrix SNP arrays"],"prefix":"10.1093","volume":"23","author":[{"given":"Andr\u00e9","family":"M\u00fcller","sequence":"first","affiliation":[{"name":"Internal Medicine I 1 \u00a0 1 \u00a0 \u00a0 Robert-Koch-Strasse 8"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karlheinz","family":"Holzmann","sequence":"additional","affiliation":[{"name":"Chip Facility\/ZKF, University of Ulm 2 \u00a0 2 \u00a0 \u00a0 D-89069 Ulm, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hans A.","family":"Kestler","sequence":"additional","affiliation":[{"name":"Internal Medicine I 1 \u00a0 1 \u00a0 \u00a0 Robert-Koch-Strasse 8"},{"name":"Neural Information Processing, University of Ulm 3 \u00a0 3 \u00a0 \u00a0 D-89069 Ulm, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,11,30]]},"reference":[{"key":"2023041109270235100_","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1186\/1479-7364-1-4-287","article-title":"Whole genome DNA copy number changes identified by high density oligonucleotide arrays","volume":"1","author":"Huang","year":"2004","journal-title":"Hum. 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Genet."},{"key":"2023041109270235100_","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1093\/bioinformatics\/btl359","article-title":"VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles","volume":"22","author":"La Rosa","year":"2006","journal-title":"Bioinformatics"},{"key":"2023041109270235100_","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1126\/science.1098918","article-title":"Large-scale copy number polymorphism in the human genome","volume":"305","author":"Sebat","year":"2004","journal-title":"Science"},{"key":"2023041109270235100_","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1186\/1471-2105-6-292","article-title":"SNP-VISTA: an interactive SNP visualization tool","volume":"6","author":"Shah","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023041109270235100_","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1086\/497343","article-title":"High-resolution identification of chromosomal abnormalities using oligonucleotide arrays containing 116,204 SNPs","volume":"77","author":"Slater","year":"2005","journal-title":"Am. J. Hum. Genet."},{"key":"2023041109270235100_","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1471-2105-7-25","article-title":"Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan","volume":"7","author":"Ting","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023041109270235100_","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1158\/0008-5472.CAN-03-2570","article-title":"Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers","volume":"64","author":"Wang","year":"2004","journal-title":"Cancer Res."},{"key":"2023041109270235100_","article-title":"Scalable Vector Graphics (SVG) 1.1 Specification","author":"World Wide Web Consortium (W3C)"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/4\/496\/49829833\/bioinformatics_23_4_496.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/23\/4\/496\/49829833\/bioinformatics_23_4_496.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T17:08:17Z","timestamp":1707412097000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/23\/4\/496\/180522"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,11,30]]},"references-count":9,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2007,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl608","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2007,2,15]]},"published":{"date-parts":[[2006,11,30]]}}}