arrayCGHbase: An Analysis Platform for Comparative Genomic Hybridization Microarrays

BMC Bioinformatics. 2005 May 23;6:124. doi: 10.1186/1471-2105-6-124.

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/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Chromosomes / ultrastructure
  • Computational Biology / methods*
  • Computer Graphics
  • Database Management Systems
  • Databases, Genetic
  • Gene Expression Profiling
  • Genes, Neoplasm
  • Genes, Reporter
  • Genome, Human
  • Genomics / methods*
  • Humans
  • Information Storage and Retrieval
  • Internet
  • Neoplasms / metabolism
  • Nucleic Acid Hybridization / methods*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Programming Languages
  • Sequence Analysis, DNA
  • Software
  • User-Computer Interface