title: TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.
abstract: BACKGROUND
  As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data.
  
  
  METHODS
  We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated search engine supporting several Boolean operators (http://tagc.univ-mrs.fr/tbrowser/). User can search and analyze TS containing a list of identifiers (gene symbols or AffyIDs) or associated with a set of functional terms.
  
  
  CONCLUSIONS
  As proof of principle, TBrowser was used to define breast cancer cell specific genes and to detect chromosomal abnormalities in tumors. Finally, taking advantage of our large collection of transcriptional signatures, we constructed a comprehensive map that summarizes gene-gene co-regulations observed through all the experiments performed on HGU133A Affymetrix platform. We provide evidences that this map can extend our knowledge of cellular signaling pathways.
authors.affiliation: Inserm U928, TAGC, Parc Scientifique de Luminy, Marseille, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Lopez
authors.forename: Julien
authors.initials: J
authors.lastname: Textoris
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bergon
authors.forename: Gilles
authors.initials: G
authors.lastname: Didier
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Remy
authors.forename: Samuel
authors.initials: S
authors.lastname: Granjeaud
authors.forename: Jean
authors.initials: J
authors.lastname: Imbert
authors.forename: Catherine
authors.initials: C
authors.lastname: Nguyen
authors.forename: Denis
authors.initials: D
authors.lastname: Puthier
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D030541:Databases, Genetic; D004526:Efficiency; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000502:physiology; D006801:Humans; D015201:Meta-Analysis as Topic; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D015398:Signal Transduction / Q000235:genetics; D012984:Software; D014584:User-Computer Interface