High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).
复制标题
DOI：
10.1186/1471-2105-6-168
复制
发表时间：
2005-07-05
影响因子：
3
通讯作者：
Weinstein JN
中科院分区：
文献类型：
--
作者：
Zeeberg BR;Qin H;Narasimhan S;Sunshine M;Cao H;Kane DW;Reimers M;Stephens RM;Bryant D;Burt SK;Elnekave E;Hari DM;Wynn TA;Cunningham-Rundles C;Stewart DM;Nelson D;Weinstein JN
我们之前开发了GoMiner，这是一个组织“有趣”基因（例如，来自微阵列实验的低表达和过表达基因）列表的应用程序，用于在基因本体论的背景下进行生物学解释。GoMiner的原始版本是面向可视化和解释结果从一个单一的微阵列（或其他高通量实验平台），使用图形用户界面。虽然该版本可以用于一次检查一个微阵列的结果，但这是一项相当繁琐的任务，并且原始GoMiner不包括用于从由多个微阵列组成的实验中获得结果的全局图像的设备。我们希望提供一种计算资源，可以自动分析多个微阵列，然后将所有结果整合到有用的可导出输出文件和可视化中。我们现在介绍一个新的工具，High-Put GoMiner，它具有这些功能和其他一些功能：它（i）有效地执行任意数量的微阵列的自动批处理的计算密集型任务，（ii）产生根据重要GO类别的数量对多个微阵列结果进行等级排序的人或计算机可读报告，（iii）通过提供重要GO类别的关系的有组织的全局聚类图像图可视化来整合多个微阵列结果，（iv）提供快速形式的“错误发现率”多重比较计算，以及（v）提供用于将转录因子结合位点与基因和GO类别相关联的注释和可视化。GoMiner实现了预期的目标，即提供一种计算资源，使多个微阵列的分析自动化，并整合所有微阵列的结果。为了说明，我们展示了这种新工具的应用，以解释常见可变免疫缺陷（CVID）中改变的基因表达模式。高通量GoMiner将在广泛的应用中有用，包括时间过程的研究，多种药物治疗的评估，多个基因敲除或敲除的比较，以及从有前途的先导化合物产生的大量化学衍生物的筛选。
We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations. We now introduce a new tool, High-Throughput GoMiner, that has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human-or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories. High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. For illustration, we show an application of this new tool to the interpretation of altered gene expression patterns in Common Variable Immune Deficiency (CVID). High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound.
登录
查看更多内容
通过比较基因组杂交分析的良性和恶性双鼠相关膀胱病变的染色体畸变。
影响因子：
3.8
作者：
Fadl-Elmula, I;Kytola, S;El Leithy, M;Abdel-Hameed, M;Mandahl, N;Elagib, A;Ibrahim, M;Larsson, C;Heim, S
通讯作者：
Heim, S
影响因子：
5.8
作者：
Al-Shahrour, F;Díaz-Uriarte, R;Dopazo, J
通讯作者：
Dopazo, J
影响因子：
4.6
作者：
McQuaid, A;Tormey, VJ;Bofill, M
通讯作者：
Bofill, M
影响因子：
1.1
作者：
Samandouras, G;King, A;Kellerman, AJ
通讯作者：
Kellerman, AJ
影响因子：
2.8
作者：
Notarangelo, LD;Giliani, S;Ugazio, AG
通讯作者：
Ugazio, AG