VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles.
BACKGROUND
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


BACKGROUND
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.
La Rosa
Philippe
P
Institut Curie, Service Bioinformatique, 26 rue d'Ulm, Paris 75248 cedex 05, France.
Viara
Eric
E
Hupé
Philippe
P
Pierron
Gaëlle
G
Liva
Stéphane
S
Neuvial
Pierre
P
Brito
Isabel
I
Lair
Séverine
S
Servant
Nicolas
N
Robine
Nicolas
N
Manié
Elodie
E
Brennetot
Caroline
C
Janoueix-Lerosey
Isabelle
I
Raynal
Virginie
V
Gruel
Nadège
N
Rouveirol
Céline
C
Stransky
Nicolas
N
Stern
Marc-Henri
MH
Delattre
Olivier
O
Aurias
Alain
A
Radvanyi
François
F
Barillot
Emmanuel
E
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D003628:Database Management Systems; D030562:Databases, Protein; D018628:Gene Dosage / Q000235:genetics; D016247:Information Storage and Retrieval / Q000379:methods; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014584:User-Computer Interface
D020543:Proteome; D014157:Transcription Factors