SQUAT: A web tool to mine human, murine and avian SAGE data. - Archive ouverte HAL Accéder directement au contenu
Article Dans Une Revue BMC Bioinformatics Année : 2008

SQUAT: A web tool to mine human, murine and avian SAGE data.

Résumé

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/. 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: <>. 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.
Fichier principal
Vignette du fichier
Liris-3555.pdf (1.32 Mo) Télécharger le fichier
Origine : Fichiers éditeurs autorisés sur une archive ouverte

Dates et versions

hal-00425133 , version 1 (27-03-2017)

Identifiants

Citer

Johan Leyritz, Stéphane Schicklin, Sylvain Blachon, Céline Keime, Céline Robardet, et al.. SQUAT: A web tool to mine human, murine and avian SAGE data.. BMC Bioinformatics, 2008, 9, pp.378. ⟨10.1186/1471-2105-9-378⟩. ⟨hal-00425133⟩
428 Consultations
148 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More