WebaCGH: An interactive online tool for the analysis and display of array comparative genomic hybridisation data

Applied Bioinformatics

Volumn 5, Issue 2, 2006, Pages 125-130

  Frankenberger, Casey ^a   Wu, Xiaolin ^a   Harmon, Jerry ^a   Church, Deanna ^b   Gangi, Lisa M ^a   Munroe, David J ^a   Urzúa, Ulises ^c  

^a SAIC FREDERICK INC   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c UNIVERSITY OF CHILE   (Chile)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; DNA MICROARRAY; GENETIC ANALYSIS; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENOMICS; ONLINE SYSTEM;

ANIMALS; CHROMOSOMES; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENOME; HUMANS; INTERNET; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGRAMMING LANGUAGES; SOFTWARE; TRANSCRIPTION, GENETIC;

EID: 33744901128     PISSN: 11755636     EISSN: 11755636     Source Type: Journal    
DOI: 10.2165/00822942-200605020-00009     Document Type: Article

References (22)

1. Iafrate AJ, Feuk L, Rivera MN, et al. Detection of large-scale variation in the human genome. Nat Genet 2004 Sep; 36 (9): 949-51
2. Sebat J, Lakshmi B, Troge J, et al. Large-scale copy number polymorphism in the human genome. Science 2004 Jul 23; 305 (5683): 525-8
3. Albertson DG, Pinkel D. Genomic microarrays in human genetic disease and cancer. Hum Mol Genet 2003 Oct 15; 12 Spec. no. 2: R145-52
4. Kallioniemi A, Kallioniemi OP, Sudar D, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992 Oct 30; 258 (5083): 818-21
5. Solinas-Toldo S, Lampel S, Stilgenbauer S, et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997 Dec; 20 (4): 399-407
6. Pinkel D, Segraves R, Sudar D, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998 Oct; 20 (2): 207-11
7. Pollack JR, Perou CM, Alizadeh AA, et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999 Sep; 23 (1): 41-6
8. Bignell GR, Huang J, Greshock J, et al. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 2004 Feb; 14 (2): 287-95
9. Pollack JR, Sorlie T, Perou CM, et al. 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 Oct 1; 99 (20): 12963-8
10. Pinkel D, Albertson DG. Comparative genomic hybridization. Annu Rev Genomics Hum Genet 2005; 6: 331-54
11. Geschwind DH, Gregg J, Boone K, et al. Klinefelter's syndrome as a model of anomalous cerebral laterality: testing gene dosage in the X chromosome pseudoautosomal region using a DNA microarray. Dev Genet 1998; 23 (3): 215-29
12. Price TS, Regan R, Mott R, et al. 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 Jun 16; 33 (11): 3455-64
13. Chen W, Erdogan F, Ropers HH, et al. CGHPRO: a comprehensive data analysis tool for array CGH. BMC Bioinformatics 2005 Apr 5; 6 (1): 85
14. Hupe P, Stransky N, Thiery JP, et al. Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics 2004 Dec 12; 20 (18): 3413-22
15. Myers CL, Dunham MJ, Kung SY, et al. Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics 2004 Dec 12; 20 (18): 3533-43
16. Urzúa U, Frankenberger C, Gangi L, et al. Microarray comparative genomic hybridization profile of a murine model for epithelial ovarian cancer reveals genomic imbalances resembling human ovarian carcinomas. Tumour Biol 2005 Aug 9; 26 (5): 236-44
17. Vaquerizas JM, Dopazo J, Diaz-Uriarte R. DNMAD: web-based diagnosis and normalization for microarray data. Bioinformatics 2004 Dec 12; 20 (18): 3656-8
18. Lage JM, Leamon JH, Pejovic T, et al. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 2003 Feb; 13 (2): 294-307
19. Colantuoni C, Henry G, Zeger S, et al. SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis. Bioinformatics 2002 Nov; 18 (11): 1540-1
20. Cheadle C, Vawter MP, Freed WJ, et al. Analysis of microarray data using Z score transformation. J Mol Diagn 2003 May; 5 (2): 73-81
21. Masayesva BG, Ha P, Garrett-Mayer E, et al. Gene expression alterations over large chromosomal regions in cancers include multiple genes unrelated to malignant progression. Proc Natl Acad Sci U S A 2004; 101: 8715-20
22. Furge KA, Dykema KJ, Ho C, et al. Comparison of array-based comparative genomic hybridization with gene expression-based regional expression biases to identify genetic abnormalities in hepatocellular carcinoma. BMC Genomics 2005; 6: 67