Database
SQUAT: A web tool to mine human, murine and avian SAGE data
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* Corresponding author: Olivier Gandrillon Gandrillon@cgmc.univ-lyon1.fr
1 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
2 Laboratoire d'InfoRmatique en Image et Systèmes d'information, UMR 5205 CNRS, Bâtiment Blaise Pascal, INSA Lyon, 43 bd du 11 novembre 1918, 69622, Villeurbanne Cedex, France
3 Pôle Rhône-Alpin de BioInformatique, Université de Lyon, F-69622, Université Lyon 1, Villeurbanne, Lyon, France,
BMC Bioinformatics 2008, 9:378 doi:10.1186/1471-2105-9-378
Published: 18 September 2008Abstract
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.
Description
We have developed an application called SQUAT (SAGE Querying and Analysis Tools) which is available at: http://bsmc.insa-lyon.fr/squat/ webcite. 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.
Conclusion
SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.