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

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

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

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

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

author email corresponding author email

BMC Bioinformatics 2005, 6:124doi: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.