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

VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles,10.1093/bioinformatics/btl359,Bioinformatics/computer Applic

VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles   (Citations: 49)
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Philippe La Rosa, Eric Viara, Philippe Hupé, Gaëlle Pierron, Stéphane Liva, Pierre Neuvial, Isabel Brito, Séverine Lair, Nicolas Servant, Nicolas Robine, Elodie Manié, Caroline Brennetothttp://academic.research.microsoft.com/io.ashx?type=5&id=2181372&selfId1=0&selfId2=0&maxNumber=12&query=
Motivation: Microarray-based CGH (Comparative Genomic Hybridi- zation), transcriptome arrays and other large-scale genomic techno- logies are now routinely used to generate a vast amount of genomic profiles. Exploratory analysis of this data is crucial in hel ping to under- stand 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 visuali- zation and first level analysis of molecular profiles. It is cu rrently 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 Immu- noPrecipitation 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 loo- king 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 data sets at http://bioinfo.curie.fr/vamp. The documentation is available at http://bioinfo.curie.fr/vamp/doc.
Journal: Bioinformatics/computer Applications in The Biosciences - BIOINFORMATICS , vol. 22, no. 17, pp. 2066-2073, 2006
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