{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:14:56Z","timestamp":1728360896627},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2005,6,13]],"date-time":"2005-06-13T00:00:00Z","timestamp":1118620800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0\/"},{"start":{"date-parts":[[2005,6,13]],"date-time":"2005-06-13T00:00:00Z","timestamp":1118620800000},"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>Chromosomal copy number changes (aneuploidies) play a key role in cancer progression and molecular evolution. These copy number changes can be studied using microarray-based comparative genomic hybridization (array CGH) or gene expression microarrays. However, accurate identification of amplified or deleted regions requires a combination of visual and computational analysis of these microarray data.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We have developed ChARMView, a visualization and analysis system for guided discovery of chromosomal abnormalities from microarray data. Our system facilitates manual or automated discovery of aneuploidies through dynamic visualization and integrated statistical analysis. ChARMView can be used with array CGH and gene expression microarray data, and multiple experiments can be viewed and analyzed simultaneously.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusion<\/jats:title>\n                        <jats:p>ChARMView is an effective and accurate visualization and analysis system for recognizing even small aneuploidies or subtle expression biases, identifying recurring aberrations in sets of experiments, and pinpointing functionally relevant copy number changes. ChARMView is freely available under the GNU GPL at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/function.princeton.edu\/ChARMView\">http:\/\/function.princeton.edu\/ChARMView<\/jats:ext-link>.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-6-146","type":"journal-article","created":{"date-parts":[[2005,6,14]],"date-time":"2005-06-14T06:13:40Z","timestamp":1118729620000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Visualization-based discovery and analysis of genomic aberrations in microarray data"],"prefix":"10.1186","volume":"6","author":[{"given":"Chad L","family":"Myers","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xing","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olga G","family":"Troyanskaya","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2005,6,13]]},"reference":[{"issue":"22","key":"471_CR1","first-page":"8143","volume":"61","author":"J Phillips","year":"2001","unstructured":"Phillips J, Hayward SW, Wang Y, Vasselli J, Pavlovich C, Padilla-Nash H, Pezullo JR, Ghadimi BM, Grossfeld GD, Rivera A, Linehan WM, Cunha GR, Ried T: The consequences of chromosomal aneuploidy on gene expression profiles in a cell line model for prostate carcinogenesis. Cancer Res 2001, 61(22):8143\u20138149.","journal-title":"Cancer Res"},{"issue":"12","key":"471_CR2","doi-asserted-by":"publisher","first-page":"M57","DOI":"10.1016\/S0962-8924(99)01661-X","volume":"9","author":"DP Cahill","year":"1999","unstructured":"Cahill DP, Kinzler K, Vogelstein B, Lengauer C: Genetic instability and darwinian selection in tumours. Trends Cell Biol 1999, 9(12):M57-M60. 10.1016\/S0962-8924(99)01661-X","journal-title":"Trends Cell Biol"},{"issue":"6785","key":"471_CR3","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/35013058","volume":"405","author":"G Fischer","year":"2000","unstructured":"Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ: Chromosomal evolution in Saccharomyces. Nature 2000, 405(6785):451\u2013454. 10.1038\/35013058","journal-title":"Nature"},{"issue":"4","key":"471_CR4","doi-asserted-by":"publisher","first-page":"2164","DOI":"10.1073\/pnas.032680899","volume":"99","author":"H Hendrickson","year":"2002","unstructured":"Hendrickson H, Slechta ES, Bergthorsson U, Andersson DI, Roth JR: Amplification-mutagenesis: Evidence that \"directed\" adaptive mutation and general hypermutability result from growth with a selected gene amplification. PNAS 2002, 99(4):2164\u20132169. 10.1073\/pnas.032680899","journal-title":"PNAS"},{"issue":"25","key":"471_CR5","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. PNAS 2002, 99(25):16144\u201316149. 10.1073\/pnas.242624799","journal-title":"PNAS"},{"issue":"1","key":"471_CR6","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/12640","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. Nat Genet 1999, 23(1):41\u201346. 10.1038\/12640","journal-title":"Nat Genet"},{"issue":"2","key":"471_CR7","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/2524","volume":"20","author":"D Pinkel","year":"1998","unstructured":"Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20(2):207\u2013211. 10.1038\/2524","journal-title":"Nat Genet"},{"issue":"11","key":"471_CR8","first-page":"2993","volume":"62","author":"B Fritz","year":"2002","unstructured":"Fritz B, Schubert F, Wrobel G, Schwaenen C, Wessendorf S, Nessling M, Korz C, Rieker R, Montgomery K, Kucherlapati R, Mechtersheimer G, Eils R, Joos S, Lichter P: Microarray-based copy number and expression profiling in dedifferentiated pleomorphic liposarcoma. Cancer Res 2002, 62(11):2993\u20132998.","journal-title":"Cancer Res"},{"key":"471_CR9","first-page":"123","volume":"1","author":"R Haddad","year":"2002","unstructured":"Haddad R, Furge KA, Miller J, Haab BB, Schoumans J: Genomic profiling and cDNA microarray analysis of human colon adenocarcinoma and associated intraperitoneal metastases reveals consistent cytogenetic and transcriptional aberrations associated with progression of multiple metastases. Applied Genomics and Proteomics 2002, 1: 123\u2013134.","journal-title":"Applied Genomics and Proteomics"},{"issue":"3","key":"471_CR10","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. Nat Genet 2000, 25(3):333\u2013337. 10.1038\/77116","journal-title":"Nat Genet"},{"issue":"1","key":"471_CR11","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1186\/1471-2105-5-151","volume":"5","author":"IA Awad","year":"2004","unstructured":"Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G: Caryoscope: An Open Source Java application for viewing microarray data in a genomic context. BMC Bioinformatics 2004, 5(1):151. 10.1186\/1471-2105-5-151","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"471_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. Genome Res 2004, 14(1):179\u2013187. 10.1101\/gr.1847304","journal-title":"Genome Res"},{"issue":"17","key":"471_CR13","doi-asserted-by":"publisher","first-page":"3246","DOI":"10.1093\/bioinformatics\/bth349","volume":"20","author":"AJ Saldanha","year":"2004","unstructured":"Saldanha AJ: Java Treeview. Bioinformatics 2004, 20(17):3246\u20133248. 10.1093\/bioinformatics\/bth349","journal-title":"Bioinformatics"},{"issue":"1","key":"471_CR14","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 \u2013 a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformatics 2004, 5(1):13. 10.1186\/1471-2105-5-13","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"471_CR15","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1109\/TSE.2004.44","volume":"30","author":"BB Bederson","year":"2004","unstructured":"Bederson BB, Grosjean J, Meyer J: Toolkit design for interactive structured graphics. Ieee Transactions on Software Engineering 2004, 30(8):535\u2013546. 10.1109\/TSE.2004.44","journal-title":"Ieee Transactions on Software Engineering"},{"issue":"18","key":"471_CR16","doi-asserted-by":"publisher","first-page":"3533","DOI":"10.1093\/bioinformatics\/bth440","volume":"20","author":"CL Myers","year":"2004","unstructured":"Myers CL, Dunham MJ, Kung SY, Troyanskaya OG: Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics 2004, 20(18):3533\u20133543.","journal-title":"Bioinformatics"},{"key":"471_CR17","volume-title":"Statistical Methods for Research Workers","author":"R Fisher","year":"1932","unstructured":"Fisher R: Statistical Methods for Research Workers. 4th edition. London: Oliver and Boyd; 1932.","edition":"4"},{"issue":"20","key":"471_CR18","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. Proc Natl Acad Sci U S A 2002, 99(20):12963\u201312968. 10.1073\/pnas.162471999","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"14","key":"471_CR19","doi-asserted-by":"publisher","first-page":"8418","DOI":"10.1073\/pnas.0932692100","volume":"100","author":"T Sorlie","year":"2003","unstructured":"Sorlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lonning PE, Brown PO, Borresen-Dale AL, Botstein D: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A 2003, 100(14):8418\u20138423. 10.1073\/pnas.0932692100","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"24","key":"471_CR20","first-page":"8861","volume":"63","author":"K Rennstam","year":"2003","unstructured":"Rennstam K, Ahlstedt-Soini M, Baldetorp B, Bendahl PO, Borg A, Karhu R, Tanner M, Tirkkonen M, Isola J: Patterns of chromosomal imbalances defines subgroups of breast cancer with distinct clinical features and prognosis. A study of 305 tumors by comparative genomic hybridization. Cancer Res 2003, 63(24):8861\u20138868.","journal-title":"Cancer Res"},{"issue":"16","key":"471_CR21","first-page":"4519","volume":"60","author":"F Forozan","year":"2000","unstructured":"Forozan F, Mahlamaki EH, Monni O, Chen Y, Veldman R, Jiang Y, Gooden GC, Ethier SP, Kallioniemi A, Kallioniemi OP: Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data. Cancer Res 2000, 60(16):4519\u20134525.","journal-title":"Cancer Res"},{"issue":"22","key":"471_CR22","first-page":"8235","volume":"61","author":"P Kauraniemi","year":"2001","unstructured":"Kauraniemi P, Barlund M, Monni O, Kallioniemi A: New amplified and highly expressed genes discovered in the ERBB2 amplicon in breast cancer by cDNA microarrays. Cancer Res 2001, 61(22):8235\u20138240.","journal-title":"Cancer Res"},{"issue":"5","key":"471_CR23","doi-asserted-by":"publisher","first-page":"1979","DOI":"10.1016\/S0002-9440(10)63556-0","volume":"163","author":"P Kauraniemi","year":"2003","unstructured":"Kauraniemi P, Kuukasjarvi T, Sauter G, Kallioniemi A: Amplification of a 280-kilobase core region at the ERBB2 locus leads to activation of two hypothetical proteins in breast cancer. Am J Pathol 2003, 163(5):1979\u20131984.","journal-title":"Am J Pathol"},{"issue":"6","key":"471_CR24","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1093\/bioinformatics\/bti113","volume":"21","author":"OC Lingjaerde","year":"2005","unstructured":"Lingjaerde OC, Baumbusch LO, Liestol K, Glad IK, Borresen-Dale AL: CGH-Explorer: a program for analysis of array-CGH data. Bioinformatics 2005, 21(6):821\u2013822. 10.1093\/bioinformatics\/bti113","journal-title":"Bioinformatics"},{"issue":"1","key":"471_CR25","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1186\/1471-2105-6-85","volume":"6","author":"W Chen","year":"2005","unstructured":"Chen W, Erdogan F, Ropers HH, Lenzner S, Ullmann R: CGHPRO \u2013 a comprehensive data analysis tool for array CGH. BMC Bioinformatics 2005, 6(1):85. 10.1186\/1471-2105-6-85","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"471_CR26","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1093\/biostatistics\/kxh017","volume":"6","author":"P Wang","year":"2005","unstructured":"Wang P, Kim Y, Pollack J, Narasimhan B, Tibshirani R: A method for calling gains and losses in array CGH data. Biostatistics 2005, 6(1):45\u201358. 10.1093\/biostatistics\/kxh017","journal-title":"Biostatistics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-146.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/1471-2105-6-146\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-6-146.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,7]],"date-time":"2024-10-07T12:12:56Z","timestamp":1728303176000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-6-146"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,6,13]]},"references-count":26,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2005,12]]}},"alternative-id":["471"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-6-146","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2005,6,13]]},"assertion":[{"value":"21 December 2004","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 June 2005","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 June 2005","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"146"}}