Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database.
Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database.
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DOI：
10.1186/1471-2105-11-421
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发表时间：
2010-08-10
影响因子：
3
通讯作者：
Hsu IC
中科院分区：
文献类型：
--
作者：
Cheng WC;Tsai ML;Chang CW;Huang CL;Chen CR;Shu WY;Lee YS;Wang TH;Hong JH;Li CY;Hsu IC
在过去的十年中，基因表达微阵列研究极大地扩展了我们对人类疾病遗传机制的认识。通过整合来自多个研究的有价值信息，对大量累积数据进行荟萃分析，在微阵列研究中变得越来越重要。然而，从公共微阵列存储库中收集特别感兴趣的数据通常会出现重大的实际问题。此外，纳入低质量的数据可能会显著降低meta分析的效率。M2DB是一个人工管理的微阵列数据库，基于临床信息，用于原始或统一预处理数据的交互式检索，以及一组质量控制指标，可轻松查询。该数据库包含超过10,000个先前发表的Affymetrix基因芯片阵列，使用人类临床标本进行。M2DB允许根据描述疾病状态和采样位置的五个临床注释的灵活组合进行在线查询。这些注释是由受控词汇表手工编排的，基于从GEO、ArrayExpress和已发表的论文中获得的信息。对于基于数组的评估控制，在线查询提供了使用三种可用的QC算法生成的QC度量集。数据质量差的数组可以很容易地从查询接口中排除。该查询提供了用于基于基因的过滤的两种算法的值，以及用于下载的原始数据和三种预处理数据。M2DB利用用户友好的QC参数界面、样本临床注释和数据格式来帮助用户获取临床元数据。该数据库提供了较低的入门门槛和整合的元分析过程。我们希望本研究能够促进微阵列meta分析的进一步发展。
Over the past decade, gene expression microarray studies have greatly expanded our knowledge of genetic mechanisms of human diseases. Meta-analysis of substantial amounts of accumulated data, by integrating valuable information from multiple studies, is becoming more important in microarray research. However, collecting data of special interest from public microarray repositories often present major practical problems. Moreover, including low-quality data may significantly reduce meta-analysis efficiency. M2DB is a human curated microarray database designed for easy querying, based on clinical information and for interactive retrieval of either raw or uniformly pre-processed data, along with a set of quality-control metrics. The database contains more than 10,000 previously published Affymetrix GeneChip arrays, performed using human clinical specimens. M2DB allows online querying according to a flexible combination of five clinical annotations describing disease state and sampling location. These annotations were manually curated by controlled vocabularies, based on information obtained from GEO, ArrayExpress, and published papers. For array-based assessment control, the online query provides sets of QC metrics, generated using three available QC algorithms. Arrays with poor data quality can easily be excluded from the query interface. The query provides values from two algorithms for gene-based filtering, and raw data and three kinds of pre-processed data for downloading. M2DB utilizes a user-friendly interface for QC parameters, sample clinical annotations, and data formats to help users obtain clinical metadata. This database provides a lower entry threshold and an integrated process of meta-analysis. We hope that this research will promote further evolution of microarray meta-analysis.
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影响因子：
14.9
作者：
Ivliev, Alexander E.;'t Hoen, Peter A. C.;Villerius, Michel P.;den Dunnen, Johan T.;Brandt, Bernd W.
通讯作者：
Brandt, Bernd W.
影响因子：
14.9
作者：
Faith JJ;Driscoll ME;Fusaro VA;Cosgrove EJ;Hayete B;Juhn FS;Schneider SJ;Gardner TS
通讯作者：
Gardner TS
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
3.5
作者：
Cahan, Patrick;Rovegno, Felicia;McCaffrey, Timothy A.
通讯作者：
McCaffrey, Timothy A.
影响因子：
45.3
作者：
Griffith, Obi L.;Melck, Adrienne;Wiseman, Sam M.
通讯作者：
Wiseman, Sam M.