Leyritz Johan, Schicklin Stéphane, Blachon Sylvain, Keime Céline, Robardet Céline, Boulicaut Jean-François, Besson Jérémy, Pensa Ruggero G, Gandrillon Olivier
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.
BMC Bioinformatics. 2008 Sep 18;9:378. doi: 10.1186/1471-2105-9-378.
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.
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.
SQUAT is a user-friendly information retrieval platform, which aims at bringing some of the state-of-the-art mining tools to biologists.
转录组研究对基因表达数据和模式仓库的需求日益增长。在这些仓库中整合原始转录组数据以及这些数据中编码的一些属性（如局部模式）非常重要。
我们开发了一个名为SQUAT（SAGE查询与分析工具）的应用程序，可在以下网址获取：http://bsmc.insa-lyon.fr/squat/。该数据库提供了三种物种（人类、小鼠和鸡）的原始SAGE数据以及从这些数据中挖掘出的模式。该数据库允许进行简单查询，如“我感兴趣的基因在哪些生物学情况下表达？”，也允许进行更复杂的查询，如“在给定生物学情况下，哪些基因经常与我感兴趣的基因共同过度表达？”。与外部网络数据库的连接丰富了生物学解释，并支持复杂查询。为了说明SQUAT的功能，我们展示并分析了三个不同查询的结果，其中一个查询得出了一个经实验验证的生物学假设。
SQUAT是一个用户友好型信息检索平台，旨在为生物学家提供一些最先进的挖掘工具。
