GO PaD: the Gene Ontology Partition Database.
GO PaD: the Gene Ontology Partition Database.
复制标题
DOI：
10.1093/nar/gkl799
复制
发表时间：
2007-01
影响因子：
14.9
通讯作者：
Ramoni MF
中科院分区：
文献类型：
--
作者：
Alterovitz G;Xiang M;Mohan M;Ramoni MF
基因本体（GO）已被广泛用于推断与基因集相关的功能意义，以便在大规模遗传研究中自动发现。GO的直接非循环图结构中的级别通常被假设为指示其术语的具体性，尽管其他工作表明这种假设并不成立。不幸的是，基于相同水平的节点的生物功能的定量分析（如在基因富集分析工具中常见的）可能导致不正确的结论以及由于可用信息的低效使用而错过的发现。本文解决了这些问题，使用信息理论的方法编码在GO分区数据库，保证最大限度地提高基因富集分析的信息。GO分区数据库被设计为具有相似特异性的GO术语的本体分区。GO分区包含不同数量的节点，并提供相关的信息论统计数据，因此研究人员可以选择以任意特定级别分析数据集。基因组分区资料库载有基因组分区集，可供分析人类及其他10种常用生物的基因功能，共有131 972个基因。该网站还包括一个在线教程。
Gene Ontology (GO) has been widely used to infer functional significance associated with sets of genes in order to automate discoveries within large-scale genetic studies. A level in GO's direct acyclic graph structure is often assumed to be indicative of its terms' specificities, although other work has suggested this assumption does not hold. Unfortunately, quantitative analysis of biological functions based on nodes at the same level (as is common in gene enrichment analysis tools) can lead to incorrect conclusions as well as missed discoveries due to inefficient use of available information. This paper addresses these using an informational theoretic approach encoded in the GO Partition Database that guarantees to maximize information for gene enrichment analysis. The GO Partition Database was designed to feature ontology partitions with GO terms of similar specificity. The GO partitions comprise varying numbers of nodes and present relevant information theoretic statistics, so researchers can choose to analyze datasets at arbitrary levels of specificity. The GO Partition Database, featuring GO partition sets for functional analysis of genes from human and 10 other commonly studied organisms with a total of 131 972 genes, is available on the internet at: . The site also includes an online tutorial.
登录
查看更多内容
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：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R
影响因子：
--
作者：
SHANNON, CE
通讯作者：
SHANNON, CE
影响因子：
14.9
作者：
Mewes, HW;Amid, C;Ruepp, A
通讯作者：
Ruepp, A
影响因子：
14.9
作者：
Keseler IM;Collado-Vides J;Gama-Castro S;Ingraham J;Paley S;Paulsen IT;Peralta-Gil M;Karp PD
通讯作者：
Karp PD