title: SQUAT: A web tool to mine human, murine and avian SAGE data.
abstract: BACKGROUND
  There is an increasing need in transcriptome research for gene expression data and pattern warehouses. It is of importance to integrate in these warehouses both raw transcriptomic data, as well as some properties encoded in these data, like local patterns.
  
  
  METHODS
  We have developed an application called SQUAT (SAGE Querying and Analysis Tools) which is available at: http://bsmc.insa-lyon.fr/squat/. This database gives access to both raw SAGE data and patterns mined from these data, for three species (human, mouse and chicken). This database allows to make simple queries like "In which biological situations is my favorite gene expressed?" as well as much more complex queries like: <<what are the genes that are frequently co-over-expressed with my gene of interest in given biological situations?>>. Connections with external web databases enrich biological interpretations, and enable sophisticated queries. To illustrate the power of SQUAT, we show and analyze the results of three different queries, one of which led to a biological hypothesis that was experimentally validated.
  
  
  CONCLUSIONS
  SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.
authors.affiliation: Equipe Bases Moléculaires de l'Autorenouvellement et de ses Altérations, Université de Lyon, F-69622, Université Lyon 1, Villeurbanne, CNRS, UMR5534, Centre de Génétique Moléculaire et Cellualire, Lyon, France. jleyritz@gmail.com
authors.forename: Johan
authors.initials: J
authors.lastname: Leyritz
authors.forename: Stéphane
authors.initials: S
authors.lastname: Schicklin
authors.forename: Sylvain
authors.initials: S
authors.lastname: Blachon
authors.forename: Céline
authors.initials: C
authors.lastname: Keime
authors.forename: Céline
authors.initials: C
authors.lastname: Robardet
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Boulicaut
authors.forename: Jérémy
authors.initials: J
authors.lastname: Besson
authors.forename: Ruggero G
authors.initials: RG
authors.lastname: Pensa
authors.forename: Olivier
authors.initials: O
authors.lastname: Gandrillon
mesh_terms: D000465:Algorithms; D000818:Animals; D001717:Birds; D003628:Database Management Systems; D030541:Databases, Genetic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D051379:Mice; D012984:Software; D014157:Transcription Factors / Q000235:genetics*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors
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