CGHPRO - A comprehensive data analysis tool for array CGH

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Chen, Wei ^a   Erdogan, Fikret ^a   Ropers, H Hilger ^a   Lenzner, Steffen ^a   Ullmann, Reinhard ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CLINICAL APPLICATION; COMPARATIVE GENOMIC HYBRIDISATION; COMPUTATIONAL ENVIRONMENTS; GRAPHICAL REPRESENTATIONS; HIDDEN MARKOV MODELING ALGORITHMS; NORMALIZATION METHODS; SEGMENTAL DUPLICATIONS; STAND-ALONE JAVA APPLICATIONS;

CLONING; COMPUTER OPERATING SYSTEMS; DATA VISUALIZATION; DNA; GENES; HIDDEN MARKOV MODELS; HOSPITAL DATA PROCESSING; OLIGONUCLEOTIDES; TISSUE; TOOLS;

DIGITAL STORAGE;

ALGORITHM; ARTICLE; CHROMOSOME DUPLICATION; CLONE; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; EQUIPMENT DESIGN; HUMAN; IMAGE ANALYSIS; IMAGE DISPLAY; INFORMATION PROCESSING; MATHEMATICAL MODEL; PROTECTION; BACTERIAL ARTIFICIAL CHROMOSOME; BIOLOGY; CHEMISTRY; CHROMOSOME; CHROMOSOME ABERRATION; CHROMOSOME DISORDER; CHROMOSOME MAP; COMPUTER LANGUAGE; COMPUTER SIMULATION; DNA MICROARRAY; FEMALE; GENOME; HUMAN GENOME; IMAGE PROCESSING; INTERNET; MALE; NUCLEIC ACID HYBRIDIZATION; PROBABILITY; PROCEDURES; SEX DIFFERENCE; STATISTICAL ANALYSIS; ULTRASTRUCTURE;

DNA;

ALGORITHMS; CHROMOSOME ABERRATIONS; CHROMOSOME DISORDERS; CHROMOSOME MAPPING; CHROMOSOMES; CHROMOSOMES, ARTIFICIAL, BACTERIAL; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; DNA; FEMALE; GENOME; GENOME, HUMAN; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; INTERNET; MALE; MARKOV CHAINS; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGRAMMING LANGUAGES; SEX FACTORS; SOFTWARE; SOFTWARE DESIGN;

EID: 22844435668     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-85     Document Type: Article

References (22)

1. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992, 258:818-821.
2. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P: Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997, 20:399-407.
3. 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, 20:207-211.
4. Ishkanian AS, Malloff CA, Watson SK, DeLeeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, MacAulay C, Lam WL: A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004, 36:299-303.
5. Fridlyand J, Snijders AM, Pinkel D, Albertson DG, Jain A: Hidden Markov models approach to the analysis of array CGH data. Journal of Multivariate Analysis 2004, 90:132-153.
6. Olshen AB, Venkatraman ES, Lucito R, Wigler M: Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5:557-572.
7. Autio R, Hautaniemi S, Kauraniemi P, Yli-Harja O, Astola J, Wolf M, Kallioniemi A: CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics 2003, 19:1714-1715.
8. Chi B, DeLeeuw RJ, Coe BP, MacAulay C, Lam WL: SeeGH - a software tool for visualization of whole genome array comparative genomic hybridization data. BMC Bioinformatics 2004, 5:13.
9. BioConductor [http://www.bioconductor.org]
10. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29:365-371.
11. Human Genome Browser Gateway [http://genome.ucsc.edu/cgi-bin/hgGateway]
12. Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, Carter NP: DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones. Genes Chromosomes Cancer 2003, 36:361-374.
13. Osoegawa K, Mammoser AG, Wu C, Frengen E, Zeng C, Catanese JJ, de Jong PJ: A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res 2001, 11:483-496.
14. Krzywinski M, Bosdet I, Smailus D, Chiu R, Mathewson C, Wye N, Barber S, Brown-John M, Chan S, Chand S, Cloutier A, Girn N, Lee D, Masson A, Mayo M, Olson T, Pandoh P, Prabhu AL, Schoenmakers E, Tsai M, Albertson D, Lam W, Choy CO, Osoegawa K, Zhao S, de Jong PJ, Schein J, Jones S, Marra MA: A set of BAC clones spanning the human genome. Nucleic Acids Res 2004, 32:3651-3660.
15. MPI array CGH protocols http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/ ProtocolsEntry.html
16. arrayCGHbase- Matrix CGH Reloaded [http://medgen.ugent.be/arrayCGHbase/]
17. L'Institut Curie: Bioinformatics http://www.curie.fr/recherche/themes/detail_equipecfm/ lang/_gb/id_equipe/303htm
18. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002, 30:e15.
19. Cleveland WS: Robust Locally Weighted Regression and Smoothing Scatterplots. Journal of the American Statistical Association 1979, 74:829-836.
20. Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE: Recent segmental duplications in the human genome. Science 2002, 297:1003-1007.
21. Locke DP, Segraves R, Nicholls RD, Schwartz S, Pinkel D, Albertson DG, Eichler EE: BAC microarray analysis of 15q11-q13 rearrangements and the impact of segmental duplications. J Med Genet 2004, 41:175-182.
22. Stankiewicz P, Lupski JR: Genome architecture, rearrangements and genomic disorders. Trends Genet 2002, 18:74-82.