{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:36:21Z","timestamp":1767962181011,"version":"3.49.0"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,10,7]],"date-time":"2008-10-07T00:00:00Z","timestamp":1223337600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"DOI":"10.1186\/1471-2105-9-422","type":"journal-article","created":{"date-parts":[[2008,10,7]],"date-time":"2008-10-07T18:19:26Z","timestamp":1223403566000},"source":"Crossref","is-referenced-by-count":30,"title":["SIGMA2: A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes"],"prefix":"10.1186","volume":"9","author":[{"given":"Raj","family":"Chari","sequence":"first","affiliation":[]},{"given":"Bradley P","family":"Coe","sequence":"additional","affiliation":[]},{"given":"Craig","family":"Wedseltoft","sequence":"additional","affiliation":[]},{"given":"Marie","family":"Benetti","sequence":"additional","affiliation":[]},{"given":"Ian M","family":"Wilson","sequence":"additional","affiliation":[]},{"given":"Emily A","family":"Vucic","sequence":"additional","affiliation":[]},{"given":"Calum","family":"MacAulay","sequence":"additional","affiliation":[]},{"given":"Raymond T","family":"Ng","sequence":"additional","affiliation":[]},{"given":"Wan L","family":"Lam","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,10,7]]},"reference":[{"key":"2407_CR1","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1186\/1476-4598-3-9","volume":"3","author":"C Garnis","year":"2004","unstructured":"Garnis C, Buys TP, Lam WL: Genetic alteration and gene expression modulation during cancer progression. Mol Cancer 2004, 3: 9. 10.1186\/1476-4598-3-9","journal-title":"Mol Cancer"},{"issue":"3","key":"2407_CR2","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1038\/ng1307","volume":"36","author":"AS Ishkanian","year":"2004","unstructured":"Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, et al.: A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004, 36(3):299\u2013303. 10.1038\/ng1307","journal-title":"Nat Genet"},{"issue":"8","key":"2407_CR3","doi-asserted-by":"publisher","first-page":"1046","DOI":"10.1101\/gr.5273806","volume":"16","author":"B Khulan","year":"2006","unstructured":"Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, et al.: Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res 2006, 16(8):1046\u20131055. 10.1101\/gr.5273806","journal-title":"Genome Res"},{"issue":"2","key":"2407_CR4","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1038\/sj.ejhg.5201531","volume":"14","author":"WW Lockwood","year":"2006","unstructured":"Lockwood WW, Chari R, Chi B, Lam WL: Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet 2006, 14(2):139\u2013148. 10.1038\/sj.ejhg.5201531","journal-title":"Eur J Hum Genet"},{"issue":"16","key":"2407_CR5","doi-asserted-by":"publisher","first-page":"7939","DOI":"10.1158\/0008-5472.CAN-06-1888","volume":"66","author":"T Rauch","year":"2006","unstructured":"Rauch T, Li H, Wu X, Pfeifer GP: MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 2006, 66(16):7939\u20137947. 10.1158\/0008-5472.CAN-06-1888","journal-title":"Cancer Res"},{"issue":"8","key":"2407_CR6","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1038\/ng1598","volume":"37","author":"M Weber","year":"2005","unstructured":"Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D: Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005, 37(8):853\u2013862. 10.1038\/ng1598","journal-title":"Nat Genet"},{"key":"2407_CR7","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1186\/1471-2164-7-324","volume":"7","author":"R Chari","year":"2006","unstructured":"Chari R, Lockwood WW, Coe BP, Chu A, Macey D, Thomson A, Davies JJ, MacAulay C, Lam WL: SIGMA: a system for integrative genomic microarray analysis of cancer genomes. BMC Genomics 2006, 7: 324. 10.1186\/1471-2164-7-324","journal-title":"BMC Genomics"},{"key":"2407_CR8","doi-asserted-by":"crossref","unstructured":"Conde L, Montaner D, Burguet-Castell J, Tarraga J, Medina I, Al-Shahrour F, Dopazo J: ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res 2007, (35 Web Server):W81\u201385. 10.1093\/nar\/gkm257","DOI":"10.1093\/nar\/gkm257"},{"issue":"17","key":"2407_CR9","doi-asserted-by":"publisher","first-page":"2066","DOI":"10.1093\/bioinformatics\/btl359","volume":"22","author":"P La Rosa","year":"2006","unstructured":"La Rosa P, Viara E, Hupe P, Pierron G, Liva S, Neuvial P, Brito I, Lair S, Servant N, Robine N, et al.: VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinformatics 2006, 22(17):2066\u20132073. 10.1093\/bioinformatics\/btl359","journal-title":"Bioinformatics"},{"key":"2407_CR10","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1186\/1471-2105-9-243","volume":"9","author":"B Chi","year":"2008","unstructured":"Chi B, deLeeuw RJ, Coe BP, Ng RT, MacAulay C, Lam WL: MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data. BMC Bioinformatics 2008, 9: 243. 10.1186\/1471-2105-9-243","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"2407_CR11","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1016\/j.ccr.2006.03.019","volume":"9","author":"DR Carrasco","year":"2006","unstructured":"Carrasco DR, Tonon G, Huang Y, Zhang Y, Sinha R, Feng B, Stewart JP, Zhan F, Khatry D, Protopopova M, et al.: High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients. Cancer Cell 2006, 9(4):313\u2013325. 10.1016\/j.ccr.2006.03.019","journal-title":"Cancer Cell"},{"issue":"6","key":"2407_CR12","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1016\/j.ccr.2006.10.009","volume":"10","author":"K Chin","year":"2006","unstructured":"Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, et al.: Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006, 10(6):529\u2013541. 10.1016\/j.ccr.2006.10.009","journal-title":"Cancer Cell"},{"issue":"12","key":"2407_CR13","doi-asserted-by":"publisher","first-page":"1927","DOI":"10.1038\/sj.bjc.6603167","volume":"94","author":"BP Coe","year":"2006","unstructured":"Coe BP, Lockwood WW, Girard L, Chari R, Macaulay C, Lam S, Gazdar AF, Minna JD, Lam WL: Differential disruption of cell cycle pathways in small cell and non-small cell lung cancer. Br J Cancer 2006, 94(12):1927\u20131935. 10.1038\/sj.bjc.6603167","journal-title":"Br J Cancer"},{"key":"2407_CR14","volume-title":"Oncogene","author":"WW Lockwood","year":"2008","unstructured":"Lockwood WW, Chari R, Coe BP, Girard L, Macaulay C, Lam S, Gazdar AF, Minna JD, Lam WL: DNA amplification is a ubiquitous mechanism of oncogene activation in lung and other cancers. Oncogene 2008."},{"issue":"6","key":"2407_CR15","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1016\/j.ccr.2006.10.008","volume":"10","author":"RM Neve","year":"2006","unstructured":"Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, et al.: A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 2006, 10(6):515\u2013527. 10.1016\/j.ccr.2006.10.008","journal-title":"Cancer Cell"},{"issue":"12","key":"2407_CR16","doi-asserted-by":"publisher","first-page":"1386","DOI":"10.1038\/ng1923","volume":"38","author":"N Stransky","year":"2006","unstructured":"Stransky N, Vallot C, Reyal F, Bernard-Pierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C, et al.: Regional copy number-independent deregulation of transcription in cancer. Nat Genet 2006, 38(12):1386\u20131396. 10.1038\/ng1923","journal-title":"Nat Genet"},{"key":"2407_CR17","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1471-2164-9-41","volume":"9","author":"MA Sanders","year":"2008","unstructured":"Sanders MA, Verhaak RG, Geertsma-Kleinekoort WM, Abbas S, Horsman S, Spek PJ, Lowenberg B, Valk PJ: SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels. BMC Genomics 2008, 9: 41. 10.1186\/1471-2164-9-41","journal-title":"BMC Genomics"},{"key":"2407_CR18","doi-asserted-by":"crossref","unstructured":"Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, et al.: The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res 2008, (36 Database):D773\u2013779.","DOI":"10.1093\/nar\/gkm966"},{"key":"2407_CR19","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1186\/1471-2105-6-274","volume":"6","author":"M Khojasteh","year":"2005","unstructured":"Khojasteh M, Lam WL, Ward RK, MacAulay C: A stepwise framework for the normalization of array CGH data. BMC Bioinformatics 2005, 6: 274. 10.1186\/1471-2105-6-274","journal-title":"BMC Bioinformatics"},{"key":"2407_CR20","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1186\/1471-2105-7-264","volume":"7","author":"P Neuvial","year":"2006","unstructured":"Neuvial P, Hupe P, Brito I, Liva S, Manie E, Brennetot C, Radvanyi F, Aurias A, Barillot E: Spatial normalization of array-CGH data. BMC Bioinformatics 2006, 7: 264. 10.1186\/1471-2105-7-264","journal-title":"BMC Bioinformatics"},{"issue":"18","key":"2407_CR21","doi-asserted-by":"publisher","first-page":"3413","DOI":"10.1093\/bioinformatics\/bth418","volume":"20","author":"P Hupe","year":"2004","unstructured":"Hupe P, Stransky N, Thiery JP, Radvanyi F, Barillot E: Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics 2004, 20(18):3413\u20133422. 10.1093\/bioinformatics\/bth418","journal-title":"Bioinformatics"},{"issue":"6","key":"2407_CR22","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1093\/bioinformatics\/btl646","volume":"23","author":"ES Venkatraman","year":"2007","unstructured":"Venkatraman ES, Olshen AB: A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007, 23(6):657\u2013663. 10.1093\/bioinformatics\/btl646","journal-title":"Bioinformatics"},{"issue":"14","key":"2407_CR23","doi-asserted-by":"publisher","first-page":"6071","DOI":"10.1158\/0008-5472.CAN-05-0465","volume":"65","author":"Y Nannya","year":"2005","unstructured":"Nannya Y, Sanada M, Nakazaki K, Hosoya N, Wang L, Hangaishi A, Kurokawa M, Chiba S, Bailey DK, Kennedy GC, et al.: A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res 2005, 65(14):6071\u20136079. 10.1158\/0008-5472.CAN-05-0465","journal-title":"Cancer Res"},{"issue":"23","key":"2407_CR24","doi-asserted-by":"publisher","first-page":"6335","DOI":"10.1093\/emboj\/cdg604","volume":"22","author":"E Ballestar","year":"2003","unstructured":"Ballestar E, Paz MF, Valle L, Wei S, Fraga MF, Espada J, Cigudosa JC, Huang TH, Esteller M: Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. Embo J 2003, 22(23):6335\u20136345. 10.1093\/emboj\/cdg604","journal-title":"Embo J"},{"issue":"3","key":"2407_CR25","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1101\/gr.4410706","volume":"16","author":"M Bibikova","year":"2006","unstructured":"Bibikova M, Lin Z, Zhou L, Chudin E, Garcia EW, Wu B, Doucet D, Thomas NJ, Wang Y, Vollmer E, et al.: High-throughput DNA methylation profiling using universal bead arrays. Genome Res 2006, 16(3):383\u2013393. 10.1101\/gr.4410706","journal-title":"Genome Res"},{"issue":"5","key":"2407_CR26","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1016\/j.ygeno.2006.12.012","volume":"89","author":"BP Coe","year":"2007","unstructured":"Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, Lam WL: Resolving the resolution of array CGH. Genomics 2007, 89(5):647\u2013653. 10.1016\/j.ygeno.2006.12.012","journal-title":"Genomics"},{"issue":"15","key":"2407_CR27","doi-asserted-by":"publisher","first-page":"1919","DOI":"10.1093\/bioinformatics\/btl269","volume":"22","author":"WN van Wieringen","year":"2006","unstructured":"van Wieringen WN, Belien JA, Vosse SJ, Achame EM, Ylstra B: ACE-it: a tool for genome-wide integration of gene dosage and RNA expression data. Bioinformatics 2006, 22(15):1919\u20131920. 10.1093\/bioinformatics\/btl269","journal-title":"Bioinformatics"},{"issue":"9","key":"2407_CR28","doi-asserted-by":"publisher","first-page":"3060","DOI":"10.1158\/0008-5472.CAN-03-3308","volume":"64","author":"X Zhao","year":"2004","unstructured":"Zhao X, Li C, Paez JG, Chin K, Janne PA, Chen TH, Girard L, Minna J, Christiani D, Leo C, et al.: An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res 2004, 64(9):3060\u20133071. 10.1158\/0008-5472.CAN-03-3308","journal-title":"Cancer Res"},{"issue":"5","key":"2407_CR29","doi-asserted-by":"publisher","first-page":"R56","DOI":"10.1186\/bcr1604","volume":"8","author":"A Grigoriadis","year":"2006","unstructured":"Grigoriadis A, Mackay A, Reis-Filho JS, Steele D, Iseli C, Stevenson BJ, Jongeneel CV, Valgeirsson H, Fenwick K, Iravani M, et al.: Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data. Breast Cancer Res 2006, 8(5):R56. 10.1186\/bcr1604","journal-title":"Breast Cancer Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-422.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-422\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-422.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,14]],"date-time":"2019-05-14T13:15:56Z","timestamp":1557839756000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-422"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,10,7]]},"references-count":29,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2407"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-422","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,10,7]]},"article-number":"422"}}