PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees.
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees.
复制标题
DOI：
10.1093/nar/gks1118
复制
发表时间：
2013-01
影响因子：
14.9
通讯作者：
Thomas PD
中科院分区：
文献类型：
--
作者：
Mi H;Muruganujan A;Thomas PD
PANTHER中的数据和工具-一个全面的，精心策划的蛋白质家族，树，亚家族和功能数据库，可在http://pantherdb.org-have上获得，十多年来经历了持续，广泛的改进。在这里，我们将描述当前的PANTHER流程作为一个整体，以及用于分析用户上传数据的网站工具。PANTHER的主要目标基本上保持不变：在大型序列数据库中准确推断（和实际应用）基因和蛋白质功能，使用系统发育树从一些模式生物的相对稀疏的实验信息中推断。然而，PANTHER的重点不断转向更准确和详细地描述基因家族史中的进化事件。这些树现在被设计为代表基因家族进化，包括对进化事件的推断，例如物种形成和基因复制。亚家族仍然被策划和用于定义HALGORITHM，但基因本体功能注释现在可以在树中的任何节点上进行，并被设计为代表祖先基因在进化过程中功能的获得和丧失。最后，PANTHER现在包括推断祖先基因的稳定数据库标识符，用于将推断的基因属性与现存物种共同祖先基因组中的特定基因相关联。
The data and tools in PANTHER—a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org—have undergone continual, extensive improvement for over a decade. Here, we describe the current PANTHER process as a whole, as well as the website tools for analysis of user-uploaded data. The main goals of PANTHER remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate from the relatively sparse experimental information from a few model organisms. Yet the focus of PANTHER has continually shifted toward more accurate and detailed representations of evolutionary events in gene family histories. The trees are now designed to represent gene family evolution, including inference of evolutionary events, such as speciation and gene duplication. Subfamilies are still curated and used to define HMMs, but gene ontology functional annotations can now be made at any node in the tree, and are designed to represent gain and loss of function by ancestral genes during evolution. Finally, PANTHER now includes stable database identifiers for inferred ancestral genes, which are used to associate inferred gene attributes with particular genes in the common ancestral genomes of extant species.
登录
查看更多内容
基因本体论：2011年的增强。
影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
4.3
作者：
Reference Genome Group of the Gene Ontology Consortium
通讯作者：
Reference Genome Group of the Gene Ontology Consortium
DOI：
10.1093/bioinformatics/bts270
发表时间：
2012-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
van Iersel MP;Villéger AC;Czauderna T;Boyd SE;Bergmann FT;Luna A;Demir E;Sorokin A;Dogrusoz U;Matsuoka Y;Funahashi A;Aladjem MI;Mi H;Moodie SL;Kitano H;Le Novère N;Schreiber F
通讯作者：
Schreiber F
影响因子：
14.9
作者：
Schaefer, Carl F.;Anthony, Kira;Buetow, Kenneth H.
通讯作者：
Buetow, Kenneth H.
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J