ArrayCGHbase: an Analysis Platform for Comparative Genomic Hybridization Microarrays

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2005 May 25

PMID 15910681

Citations 44

Authors

Bjorn Menten

Filip Pattyn

Katleen De Preter

Piet Robbrecht

Evi Michels

Karen Buysse

Geert Mortier

Anne De Paepe

Steven Van Vooren

Joris Vermeesch

Yves Moreau

Bart De Moor

Stefan Vermeulen

Frank Speleman

Jo Vandesompele

Affiliations

Soon will be listed here.

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/.

Citing Articles

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Fanconi-BRCA pathway mutations in childhood T-cell acute lymphoblastic leukemia.

Pouliot G, Degar J, Hinze L, Kochupurakkal B, Vo C, Burns M PLoS One. 2019; 14(11):e0221288.

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PRC2 loss induces chemoresistance by repressing apoptosis in T cell acute lymphoblastic leukemia.

Aries I, Bodaar K, Karim S, Chonghaile T, Hinze L, Burns M J Exp Med. 2018; 215(12):3094-3114.

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Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the mtDNA Variant Type and Load in Human Pluripotent Stem Cells.

Zambelli F, Mertens J, Dziedzicka D, Sterckx J, Markouli C, Keller A Stem Cell Reports. 2018; 11(1):102-114.

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Early-onset primary antibody deficiency resembling common variable immunodeficiency challenges the diagnosis of Wiedeman-Steiner and Roifman syndromes.

Bogaert D, Dullaers M, Kuehn H, Leroy B, Niemela J, De Wilde H Sci Rep. 2017; 7(1):3702.

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