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Bioinformatics Advance Access originally published online on July 4, 2006
Bioinformatics 2006 22(17):2066-2073; doi:10.1093/bioinformatics/btl359
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles

Philippe La Rosa 1,*, Eric Viara 1, Philippe Hupé 1,2, Gaëlle Pierron 3, Stéphane Liva 1, Pierre Neuvial 1, Isabel Brito 1, Séverine Lair 1, Nicolas Servant 1, Nicolas Robine 1,4, Elodie Manié 3, Caroline Brennetot 3, Isabelle Janoueix-Lerosey 3, Virginie Raynal 3, Nadège Gruel 3, Céline Rouveirol 2, Nicolas Stransky 2, Marc-Henri Stern 3, Olivier Delattre 3, Alain Aurias 3, François Radvanyi 2 and Emmanuel Barillot 1

1 Institut Curie, Service Bioinformatique, 26 rue d'Ulm, Paris 75248 cedex 05, France
2 Institut Curie, CNRS UMR 144, 26 rue d'Ulm, Paris 75248 cedex 05, France
3 Institut Curie, INSERM U509, 26 rue d'Ulm, Paris 75248 cedex 05, France
4 Institut Curie, CNRS Université Pierre et Marie Curie UMR 7147, 26 rue d'Ulm, Paris, 75248 cedex 05, France

*To whom correspondence should be addressed.

Motivation: Microarray-based CGH (Comparative Genomic Hybridization), transcriptome arrays and other large-scale genomic technologies are now routinely used to generate a vast amount of genomic profiles. Exploratory analysis of this data is crucial in helping to understand the data and to help form biological hypotheses. This step requires visualization of the data in a meaningful way to visualize the results and to perform first level analyses.

Results: We have developed a graphical user interface for visualization and first level analysis of molecular profiles. It is currently in use at the Institut Curie for cancer research projects involving CGH arrays, transcriptome arrays, SNP (single nucleotide polymorphism) arrays, loss of heterozygosity results (LOH), and Chromatin ImmunoPrecipitation arrays (ChIP chips). The interface offers the possibility of studying these different types of information in a consistent way. Several views are proposed, such as the classical CGH karyotype view or genome-wide multi-tumor comparison. Many functionalities for analyzing CGH data are provided by the interface, including looking for recurrent regions of alterations, confrontation to transcriptome data or clinical information, and clustering. Our tool consists of PHP scripts and of an applet written in Java. It can be run on public datasets at http://bioinfo.curie.fr/vamp

Availability: The VAMP software (Visualization and Analysis of array-CGH,transcriptome and other Molecular Profiles) is available upon request. It can be tested on public datasets at http://bioinfo.curie.fr/vamp. The documentation is available at http://bioinfo.curie.fr/vamp/doc

Contact: vamp{at}curie.fr

Received on January 11, 2006; revised on May 31, 2006; accepted on June 25, 2006

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