GECKO: a complete large-scale gene expression analysis platform.
GECKO: a complete large-scale gene expression analysis platform.
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DOI：
10.1186/1471-2105-5-195
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发表时间：
2004-12-10
影响因子：
3
通讯作者：
Bushnell S
中科院分区：
文献类型：
--
作者：
Theilhaber J;Ulyanov A;Malanthara A;Cole J;Xu D;Nahf R;Heuer M;Brockel C;Bushnell S
Gecko（基因表达：计算和知识组织）是一个完整的、高容量的集中式基因表达分析系统，是根据分布式用户社区的需求而开发的。Gecko基于客户机-服务器架构，拥有一个通常包含成千上万Affymetrix扫描的集中式存储库，包括用于从远程站点上传数据的自动处理管道、数据库、实现约50种不同分析工具的计算引擎和客户端应用程序。可用的分析工具包括聚类方法、主成分分析、包括特征选择和交叉验证在内的监督分类、多因子方差分析、统计对比计算以及用于在给定错误率或显著性水平下提取数据的各种后处理工具。由于其开放的架构，Gecko还允许集成新的算法。Gecko框架非常通用：非affymetrix和非基因表达数据也可以分析。Gecko体系结构的一个独特特性是分析树的概念（实际上是一个有向无环图），其中保存了正在进行的分析中的所有连续结果。这种方法已被证明是非常宝贵的，它允许大型（约100个用户）和分布式社区共享结果，并在数年的时间内反复返回到旧的、可能非常复杂的基因表达数据分析。Gecko系统作为免费软件公开发布。总的来说或部分来说，Gecko框架应该证明对具有广泛分析需求的用户和系统开发人员是有用的。
Gecko (Gene Expression: Computation and Knowledge Organization) is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing ~ 50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph), in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (~ 100 users) and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data. The Gecko system is being made publicly available as free software . In totality or in parts, the Gecko framework should prove useful to users and system developers with a broad range of analysis needs.
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DOI：
10.1073/pnas.091062498
发表时间：
2001-04-24
影响因子：
11.1
作者：
Tusher, VG;Tibshirani, R;Chu, G
通讯作者：
Chu, G
影响因子：
46.9
作者：
Schwikowski, B;Uetz, P;Fields, S
通讯作者：
Fields, S
影响因子：
46.9
作者：
Lockhart, DJ;Dong, HL;Brown, EL
通讯作者：
Brown, EL
影响因子：
1.7
作者：
Theilhaber, J;Bushnell, S;Fuchs, R
通讯作者：
Fuchs, R
影响因子：
12.3
作者：
Hosack DA;Dennis G Jr;Sherman BT;Lane HC;Lempicki RA
通讯作者：
Lempicki RA