Open Access Software

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

Björn Menten1, Filip Pattyn1, Katleen De Preter1, Piet Robbrecht1, Evi Michels1, Karen Buysse1, Geert Mortier1, Anne De Paepe1, Steven van Vooren2, Joris Vermeesch3, Yves Moreau2, Bart De Moor2, Stefan Vermeulen4, Frank Speleman1 and Jo Vandesompele1*

Author Affiliations

1 Center for Medical Genetics, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium

2 Department of Electrotechnical Engineering, Faculty of Applied Sciences, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium

3 Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven, Belgium

4 Hogeschool Gent, Vesalius Department of Health Care, Keramiekstraat 80, B-9000 Ghent, Belgium

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BMC Bioinformatics 2005, 6:124  doi:10.1186/1471-2105-6-124

Published: 23 May 2005

Abstract

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/ webcite.