CHESS (CgHExpreSS): A comprehensive analysis tool for the analysis of genomic alterations and their effecsts on the expression profile of the genome

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Lee, Mikyung ^a   Kim, Yangseok ^a  

^a Kyung Hee University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMIC HYBRIDIZATIONS; COMPREHENSIVE ANALYSIS; EXPERIMENTAL PLATFORM; GENE EXPRESSION LEVELS; GENE EXPRESSION PROFILING; SIMPLE LINEAR REGRESSION; SPEARMAN RANK CORRELATION; VISUALIZATION MODULES;

BIOINFORMATICS; CHROMOSOMES; COMPUTER SOFTWARE; CORRELATION METHODS; DISEASES; JAVA PROGRAMMING LANGUAGE; TOOLS;

GENE EXPRESSION;

COMPLEMENTARY DNA;

ALGORITHM; ARTICLE; BIOINFORMATICS; CLINICAL ARTICLE; COLORECTAL CANCER; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER LANGUAGE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE MUTATION; GENOME ANALYSIS; HUMAN; INTERNET; MOLECULAR PROBE; PHENOTYPE; STATISTICAL ANALYSIS; WEB BROWSER; GENOME; GENOMICS; METHODOLOGY;

GENE EXPRESSION PROFILING; GENOME; GENOMICS; SOFTWARE;

EID: 74049111290     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-424     Document Type: Article

References (15)

1. 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):139-148. 10.1038/sj.ejhg.5201531, 16288307.
2. van Beers EH, Nederlof PM. Array-CGH and breast cancer. Breast Cancer Res 2006, 8(3):210. 10.1186/bcr1510, 1557735, 16817944.
3. Diep CB, Kleivi K, Ribeiro FR, Teixeira MR, Lindgjaerde OC, Lothe RA. The order of genetic events associated with colorectal cancer progression inferred from meta-analysis of copy number changes. Genes Chromosomes Cancer 2006, 45(1):31-41. 10.1002/gcc.20261, 16145679.
4. Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, Ringner M, Sauter G, Monni O, Elkahloun A, Kallioniemi O, Kallioniemi A. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 2002, 62(21):6240-6245.
5. Tsafrir D, Bacolod M, Selvanayagam Z, Tsafrir I, Shia J, Zeng Z, Liu H, Krier C, Stengel RF, Barany F, Gerald WL, Paty PB, Domany E, Notterman DA. Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Res 2006, 66(4):2129-2137. 10.1158/0008-5472.CAN-05-2569, 16489013.
6. Kim TM, Jung YC, Rhyu MG, Jung MH, Chung YJ. GEAR: genomic enrichment analysis of regional DNA copy number changes. Bioinformatics 2008, 24(3):420-421. 10.1093/bioinformatics/btm582, 18037611.
7. Shankar G, Rossi MR, McQuaid DE, Conroy JM, Gaile DG, Cowell JK, Nowak NJ, Liang P. aCGHViewer: A Generic Visualization Tool For aCGH data. Cancer Inform 2006, 2:36-43. 1847423,1847423, 17404607.
8. Liva S, Hupe P, Neuvial P, Brito I, Viara E, La Rosa P, Barillot E. CAPweb: a bioinformatics CGH array analysis platform. Nucleic Acids Res 2006, (34 Web Server):W477-481. 10.1093/nar/gkl215, 1538852, 16845053.
9. 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):1919-1920. 10.1093/bioinformatics/btl269, 16731696.
10. 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):W81-85. 10.1093/nar/gkm257, 1933149, 17468499.
11. La Rosa P, Viara E, Hupe P, Pierron G, Liva S, Neuvial P, Brito I, Lair S, Servant N, Robine N, Manie E, Brennetot C, Janoueix-Lerosey I, Raynal V, Gruel N, Rouveirol C, Stransky N, Stern MH, Delattre O, Aurias A, Radvanyi F, Barillot E. VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles. Bioinformatics 2006, 22(17):2066-2073. 10.1093/bioinformatics/btl359, 16820431.
12. Chari R, Coe BP, Wedseltoft C, Benetti M, Wilson IM, Vucic EA, MacAulay C, Ng RT, Lam WL. SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. BMC Bioinformatics 2008, 9:422. 10.1186/1471-2105-9-422, 2571113, 18840289.
13. Fridlyand J, Snijders AM, Pinkel D, Albertson DG, Jain A. Hidden Markov models approach to the analysis of array CGH data. J Multivariate Analysis 2004, 90:132-153.
14. Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5(4):557-572. 10.1093/biostatistics/kxh008, 15475419.
15. Price TS, Regan R, Mott R, Hedman A, Honey B, Daniels RJ, Smith L, Greenfield A, Tiganescu A, Buckle V, Ventress N, Ayyub H, Salhan A, Pedraza-Diaz S, Broxholme J, Ragoussis J, Higgs DR, Flint J, Knight SJ. SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data. Nucleic Acids Res 2005, 33(11):3455-3464. 10.1093/nar/gki643, 1151590, 15961730.