PANTHER version 10: expanded protein families and functions, and analysis tools.
PANTHER version 10: expanded protein families and functions, and analysis tools.
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DOI：
10.1093/nar/gkv1194
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发表时间：
2016-01-04
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;Poudel S;Muruganujan A;Casagrande JT;Thomas PD
PANTHER（Protein Analysis Through Evolutionary Relationships，http://pantherdb.org）是一个广泛使用的在线资源，用于全面的蛋白质进化和功能分类，并包括用于大规模生物数据分析的工具。最近的发展集中在三个主要领域：基因组覆盖率，功能信息（“注释”）的覆盖率和准确性，以及改进的基因组数据分析工具。PANTHER的最新版本10.0包括近5000个新的蛋白质家族（总共超过12000个家族），每个家族都有一个参考系统发育树，包括来自104个完全测序的基因组的蛋白质编码基因，跨越所有生命王国。系统发生树现在除了物种形成和基因复制事件外，还包括水平转移事件的推断。使用基因本体系统发育注释项目生成的模型定期更新功能注释。对于数据分析工具，PANTHER扩大了可用于功能富集测试的不同“功能注释集”的数量，允许分析访问所有基因本体论注释-每月从基因本体论数据库更新-除了通过进化关系推断的注释。Prowler（数据浏览器）已经更新，使用户能够更有效地浏览整个数据库，并使用PANTHER中的多个分类轴创建自定义基因列表。
PANTHER (Protein Analysis THrough Evolutionary Relationships, http://pantherdb.org) is a widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. Recent development has been focused in three main areas: genome coverage, functional information (‘annotation’) coverage and accuracy, and improved genomic data analysis tools. The latest version of PANTHER, 10.0, includes almost 5000 new protein families (for a total of over 12 000 families), each with a reference phylogenetic tree including protein-coding genes from 104 fully sequenced genomes spanning all kingdoms of life. Phylogenetic trees now include inference of horizontal transfer events in addition to speciation and gene duplication events. Functional annotations are regularly updated using the models generated by the Gene Ontology Phylogenetic Annotation Project. For the data analysis tools, PANTHER has expanded the number of different ‘functional annotation sets’ available for functional enrichment testing, allowing analyses to access all Gene Ontology annotations—updated monthly from the Gene Ontology database—in addition to the annotations that have been inferred through evolutionary relationships. The Prowler (data browser) has been updated to enable users to more efficiently browse the entire database, and to create custom gene lists using the multiple axes of classification in PANTHER.