GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
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DOI：
10.1186/1471-2105-10-48
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发表时间：
2009-02-03
影响因子：
3
通讯作者：
Yakhini, Zohar
中科院分区：
文献类型：
--
作者：
Eden, Eran;Navon, Roy;Yakhini, Zohar
背景资料：自GO注释项目开始以来，已经开发了各种工具来支持探索和搜索GO数据库。特别地，目前可获得进行GO富集分析的各种工具。这些工具中的大多数需要作为输入的靶基因组和背景组，并寻求与背景组相比在靶组中的富集。还有一些工具支持分析排名列表。后者通常依赖于模拟或工会约束校正分配统计显着性的results.Results：GOrilla是一个基于网络的应用程序，确定丰富的GO条款排名基因列表，而不需要用户提供明确的目标和背景集。这在许多典型的情况下特别有用，其中基因组数据可以自然地表示为基因的排序列表（例如，G.通过表达水平或差异表达）。GOrilla采用灵活的阈值统计方法来发现在排名基因列表的顶部显著富集的GO术语。GOrilla建立在基础分布的完整理论表征（称为mHG）的基础上，计算所观察到的富集的精确p值，考虑到阈值多重检验而无需模拟。这使得能够以秒为单位对数千个基因和数千个GO术语进行严格的统计分析。富集分析的输出被可视化为层次结构，提供了富集的GO术语之间的关系的清晰视图。结论：GOrilla是一种高效的GO分析工具，具有独特的功能，为现有的GO富集工具库提供了有用的补充。GOrilla的独特功能和优势超过其他阈值自由丰富的工具，包括严格的统计，快速的运行时间和有效的图形表示。GOrilla可在http://cbl-gorilla.cs.technion.ac.il上公开获取
Background: Since the inception of the GO annotation project, a variety of tools have been developed that support exploring and searching the GO database. In particular, a variety of tools that perform GO enrichment analysis are currently available. Most of these tools require as input a target set of genes and a background set and seek enrichment in the target set compared to the background set. A few tools also exist that support analyzing ranked lists. The latter typically rely on simulations or on union-bound correction for assigning statistical significance to the results.Results: GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e. g. by level of expression or of differential expression). GOrilla employs a flexible threshold statistical approach to discover GO terms that are significantly enriched at the top of a ranked gene list. Building on a complete theoretical characterization of the underlying distribution, called mHG, GOrilla computes an exact p-value for the observed enrichment, taking threshold multiple testing into account without the need for simulations. This enables rigorous statistical analysis of thousand of genes and thousands of GO terms in order of seconds. The output of the enrichment analysis is visualized as a hierarchical structure, providing a clear view of the relations between enriched GO terms.Conclusion: GOrilla is an efficient GO analysis tool with unique features that make a useful addition to the existing repertoire of GO enrichment tools. GOrilla's unique features and advantages over other threshold free enrichment tools include rigorous statistics, fast running time and an effective graphical representation. GOrilla is publicly available at: http://cbl-gorilla.cs.technion.ac.il