arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

被引：73

作者：

Menten, B

Pattyn, F

De Preter, K

Robbrecht, P

Michels, E

Buysse, K

Mortier, G

De Paepe, A

van Vooren, S

Vermeesch, J

Moreau, Y

De Moor, B

Vermeulen, S

Speleman, F

Vandesompele, J

机构：

[1] Ghent Univ Hosp, Ctr Med Genet, B-9000 Ghent, Belgium

[2] Katholieke Univ Leuven, Fac Sci Appl, Dept Electrotech Engn, B-3001 Heverlee, Belgium

[3] Leuven Univ Hosp, Ctr Human Genet, B-3000 Louvain, Belgium

[4] Hogesch Gent, Vesalius Dept Hlth Care, B-9000 Ghent, Belgium

来源：

BMC BIOINFORMATICS | 2005年 / 6卷 / 1期

关键词：

D O I：

10.1186/1471-2105-6-124

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: The availability of the human genome sequence as well as the large number of physically accessible oligonucleotides, cDNA, and BAC clones across the entire genome has triggered and accelerated the use of several platforms for analysis of DNA copy number changes, amongst others microarray comparative genomic hybridization (arrayCGH). One of the challenges inherent to this new technology is the management and analysis of large numbers of data points generated in each individual experiment. Results: We have developed arrayCGHbase, a comprehensive analysis platform for arrayCGH experiments consisting of a MIAME ( Minimal Information About a Microarray Experiment) supportive database using MySQL underlying a data mining web tool, to store, analyze, interpret, compare, and visualize arrayCGH results in a uniform and user-friendly format. Following its flexible design, arrayCGHbase is compatible with all existing and forthcoming arrayCGH platforms. Data can be exported in a multitude of formats, including BED files to map copy number information on the genome using the Ensembl or UCSC genome browser. Conclusion: ArrayCGHbase is a web based and platform independent arrayCGH data analysis tool, that allows users to access the analysis suite through the internet or a local intranet after installation on a private server. ArrayCGHbase is available at http:// medgen. ugent. be/ arrayCGHbase/.

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