{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T14:36:22Z","timestamp":1761662182051},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2004,10,15]],"date-time":"2004-10-15T00:00:00Z","timestamp":1097798400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"},{"start":{"date-parts":[[2004,10,15]],"date-time":"2004-10-15T00:00:00Z","timestamp":1097798400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We have developed Caryoscope, which is an open source Java application for visualizing microarray data from array comparative genome hybridization experiments in a genomic context. Caryoscope can read General Feature Format files (GFF files), as well as comma- and tab-delimited files, that define the genomic positions of the microarray reporters for which data are obtained. The microarray data can be browsed using an interactive, zoomable interface, which helps users identify regions of chromosomal deletion or amplification. The graphical representation of the data can be exported in a number of graphic formats, including publication-quality formats such as PostScript.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>Caryoscope is a useful tool that can aid in the visualization, exploration and interpretation of microarray data in a genomic context.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-5-151","type":"journal-article","created":{"date-parts":[[2004,10,21]],"date-time":"2004-10-21T06:24:15Z","timestamp":1098339855000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Caryoscope: An Open Source Java application for viewing microarray data in a genomic context"],"prefix":"10.1186","volume":"5","author":[{"given":"Ihab AB","family":"Awad","sequence":"first","affiliation":[]},{"given":"Christian A","family":"Rees","sequence":"additional","affiliation":[]},{"given":"Tina","family":"Hernandez-Boussard","sequence":"additional","affiliation":[]},{"given":"Catherine A","family":"Ball","sequence":"additional","affiliation":[]},{"given":"Gavin","family":"Sherlock","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2004,10,15]]},"reference":[{"key":"267_CR1","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"MB Eisen","year":"1998","unstructured":"Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns.\n                           Proc Natl Acad Sci U S A 1998, 95: 14863\u201314868. 10.1073\/pnas.95.25.14863","journal-title":"Proc Natl Acad Sci U S A"},{"key":"267_CR2","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/14385","volume":"23","author":"JR Pollack","year":"1999","unstructured":"Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO: Genome-wide analysis of DNA copy-number changes using cDNA microarrays.\n                           Nat Genet 1999, 23: 41\u201346. 10.1038\/14385","journal-title":"Nat Genet"},{"key":"267_CR3","doi-asserted-by":"publisher","first-page":"RESEARCH0075","DOI":"10.1186\/gb-2002-3-12-research0075","volume":"3","author":"JJ Crawley","year":"2002","unstructured":"Crawley JJ, Furge KA: Identification of frequent cytogenetic aberrations in hepatocellular carcinoma using gene-expression microarray data.\n                           Genome Biol 2002, 3: RESEARCH0075. 10.1186\/gb-2002-3-12-research0075","journal-title":"Genome Biol"},{"key":"267_CR4","doi-asserted-by":"publisher","first-page":"333","DOI":"10.1038\/77116","volume":"25","author":"TR Hughes","year":"2000","unstructured":"Hughes TR, Roberts CJ, Dai H, Jones AR, Meyer MR, Slade D, Burchard J, Dow S, Ward TR, Kidd MJ, Friend SH, Marton MJ: Widespread aneuploidy revealed by DNA microarray expression profiling.\n                           Nat Genet 2000, 25: 333\u2013337. 10.1038\/77116","journal-title":"Nat Genet"},{"key":"267_CR5","doi-asserted-by":"publisher","first-page":"12963","DOI":"10.1073\/pnas.162471999","volume":"99","author":"JR Pollack","year":"2002","unstructured":"Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO: Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.\n                           Proc Natl Acad Sci U S A 2002, 99: 12963\u201312968. 10.1073\/pnas.162471999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"267_CR6","doi-asserted-by":"publisher","first-page":"3915","DOI":"10.1073\/pnas.0400272101","volume":"101","author":"CD Baldus","year":"2004","unstructured":"Baldus CD, Liyanarachchi S, Mrozek K, Auer H, Tanner SM, Guimond M, Ruppert AS, Mohamed N, Davuluri RV, Caligiuri MA, Bloomfield CD, de la Chapelle A: Acute myeloid leukemia with complex karyotypes and abnormal chromosome 21: Amplification discloses overexpression of APP, ETS2, and ERG genes.\n                           Proc Natl Acad Sci U S A 2004, 101: 3915\u20133920. 10.1073\/pnas.0400272101","journal-title":"Proc Natl Acad Sci U S A"},{"key":"267_CR7","doi-asserted-by":"publisher","first-page":"2383","DOI":"10.1016\/S0002-9440(10)63593-6","volume":"163","author":"SC Linn","year":"2003","unstructured":"Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks CB, van de Rijn M: Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.\n                           Am J Pathol 2003, 163: 2383\u20132395.","journal-title":"Am J Pathol"},{"key":"267_CR8","doi-asserted-by":"publisher","first-page":"16144","DOI":"10.1073\/pnas.242624799","volume":"99","author":"MJ Dunham","year":"2002","unstructured":"Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, Rosenzweig F, Botstein D: Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae.\n                           Proc Natl Acad Sci U S A 2002, 99: 16144\u201316149. 10.1073\/pnas.242624799","journal-title":"Proc Natl Acad Sci U S A"},{"key":"267_CR9","doi-asserted-by":"publisher","first-page":"RESEARCH0026","DOI":"10.1186\/gb-2002-3-6-research0026","volume":"3","author":"JY Lin","year":"2002","unstructured":"Lin JY, Pollack JR, Chou FL, Rees CA, Christian AT, Bedford JS, Brown PO, Ginsberg MH: Physical mapping of genes in somatic cell radiation hybrids by comparative genomic hybridization to cDNA microarrays.\n                           Genome Biol 2002, 3: RESEARCH0026. 10.1186\/gb-2002-3-6-research0026","journal-title":"Genome Biol"},{"key":"267_CR10","doi-asserted-by":"publisher","first-page":"R37","DOI":"10.1186\/gb-2004-5-5-r37","volume":"5","author":"RJ Baerends","year":"2004","unstructured":"Baerends RJ, Smits WK, De Jong A, Hamoen LW, Kok J, Kuipers OP: Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data.\n                           Genome Biol 2004, 5: R37. 10.1186\/gb-2004-5-5-r37","journal-title":"Genome Biol"},{"key":"267_CR11","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1471-2105-5-13","volume":"5","author":"B Chi","year":"2004","unstructured":"Chi B, DeLeeuw RJ, Coe BP, MacAulay C, Lam WL: SeeGH - A software tool for visualization of whole genome array comparative genomic hybridization data.\n                           BMC Bioinformatics 2004, 5: 13. 10.1186\/1471-2105-5-13","journal-title":"BMC Bioinformatics"},{"key":"267_CR12","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1101\/gr.1847304","volume":"14","author":"J Greshock","year":"2004","unstructured":"Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL: 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis.\n                           Genome Res 2004, 14: 179\u2013187. 10.1101\/gr.1847304","journal-title":"Genome Res"},{"key":"267_CR13","unstructured":"Java[http:\/\/java.sun.com\/]"},{"key":"267_CR14","unstructured":"Java Web Start[http:\/\/java.sun.com\/products\/javawebstart\/]"},{"key":"267_CR15","unstructured":"Caryoscope[http:\/\/caryoscope.stanford.edu\/]"},{"key":"267_CR16","unstructured":"General Feature Format (GFF)[http:\/\/www.sanger.ac.uk\/Software\/formats\/GFF\/]"},{"key":"267_CR17","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1093\/nar\/gkg014","volume":"31","author":"M Diehn","year":"2003","unstructured":"Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA: SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.\n                           Nucleic Acids Res 2003, 31: 219\u2013223. 10.1093\/nar\/gkg014","journal-title":"Nucleic Acids Res"},{"key":"267_CR18","unstructured":"Open Source Initiative (OSI)[http:\/\/www.opensource.org\/]"},{"key":"267_CR19","unstructured":"The MIT License[http:\/\/www.opensource.org\/licenses\/mit-license.php]"},{"key":"267_CR20","unstructured":"Aliasing Problems and Anti-Aliasing Techniques[http:\/\/www.siggraph.org\/education\/materials\/HyperGraph\/aliasing\/alias0.htm]"},{"key":"267_CR21","unstructured":"Digital Imaging and Communications in Medicine (DICOM)[http:\/\/medical.nema.org\/]"},{"key":"267_CR22","unstructured":"CGHAnalyzer[http:\/\/guanine.genomics.upenn.edu\/people\/faculty\/weberb\/CGH\/html\/]"},{"key":"267_CR23","unstructured":"SeeGH[http:\/\/www.bccrc.ca\/ArrayCGH\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-151.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-5-151\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-5-151.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:18:57Z","timestamp":1728303537000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-5-151"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,10,15]]},"references-count":23,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2004,12]]}},"alternative-id":["267"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-5-151","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2004,10,15]]},"assertion":[{"value":"12 May 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 October 2004","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 October 2004","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"151"}}