title: VAMP: visualization and analysis of array-CGH, transcriptome and other molecular profiles.
abstract: 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.
authors.affiliation: Institut Curie, Service Bioinformatique, 26 rue d'Ulm, Paris 75248 cedex 05, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: La Rosa
authors.forename: Eric
authors.initials: E
authors.lastname: Viara
authors.forename: Philippe
authors.initials: P
authors.lastname: Hupé
authors.forename: Gaëlle
authors.initials: G
authors.lastname: Pierron
authors.forename: Stéphane
authors.initials: S
authors.lastname: Liva
authors.forename: Pierre
authors.initials: P
authors.lastname: Neuvial
authors.forename: Isabel
authors.initials: I
authors.lastname: Brito
authors.forename: Séverine
authors.initials: S
authors.lastname: Lair
authors.forename: Nicolas
authors.initials: N
authors.lastname: Servant
authors.forename: Nicolas
authors.initials: N
authors.lastname: Robine
authors.forename: Elodie
authors.initials: E
authors.lastname: Manié
authors.forename: Caroline
authors.initials: C
authors.lastname: Brennetot
authors.forename: Isabelle
authors.initials: I
authors.lastname: Janoueix-Lerosey
authors.forename: Virginie
authors.initials: V
authors.lastname: Raynal
authors.forename: Nadège
authors.initials: N
authors.lastname: Gruel
authors.forename: Céline
authors.initials: C
authors.lastname: Rouveirol
authors.forename: Nicolas
authors.initials: N
authors.lastname: Stransky
authors.forename: Marc-Henri
authors.initials: MH
authors.lastname: Stern
authors.forename: Olivier
authors.initials: O
authors.lastname: Delattre
authors.forename: Alain
authors.initials: A
authors.lastname: Aurias
authors.forename: François
authors.initials: F
authors.lastname: Radvanyi
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
mesh_terms: 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
chemical_list: D020543:Proteome; D014157:Transcription Factors