Abstract

PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-coding genes from all domains of life. The evolutionary classification is based on a library of over 15,000 phylogenetic trees, and the functional classifications include Gene Ontology terms and pathways. Here, we analyze the current coverage of genes from genomes in different taxonomic groups, so that users can better understand what to expect when analyzing a gene list using PANTHER tools. We also describe extensive improvements to PANTHER made in the past two years. The PANTHER Protein Class ontology has been completely refactored, and 6101 PANTHER families have been manually assigned to a Protein Class, providing a high level classification of protein families and their genes. Users can access the TreeGrafter tool to add their own protein sequences to the reference phylogenetic trees in PANTHER, to infer evolutionary context as well as fine-grained annotations. We have added human enhancer-gene links that associate non-coding regions with the annotated human genes in PANTHER. We have also expanded the available services for programmatic access to PANTHER tools and data via application programming interfaces (APIs). Other improvements include additional plant genomes and an updated PANTHER GO-slim.

中文翻译：

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PANTHER 版本 16：修订的家族分类、基于树的分类工具、增强子区域和广泛的 API

摘要

PANTHER（通过进化关系进行蛋白质分析，http://www.pantherdb.org）是对来自所有生命领域的蛋白质编码基因进行进化和功能分类的资源。进化分类基于超过 15,000 个系统发育树的库，功能分类包括基因本体术语和通路。在这里，我们分析了不同分类群中基因组的当前覆盖率，以便用户在使用 PANTHER 工具分析基因列表时可以更好地理解预期结果。我们还描述了过去两年对 PANTHER 所做的广泛改进。PANTHER 蛋白质类本体已经完全重构，6101 个 PANTHER 家族被手动分配到一个蛋白质类，提供了蛋白质家族及其基因的高级分类。用户可以访问 TreeGrafter 工具，将自己的蛋白质序列添加到 PANTHER 中的参考系统发育树中，以推断进化背景以及细粒度注释。我们添加了人类增强子基因链接，将非编码区域与 PANTHER 中注释的人类基因相关联。我们还扩展了通过应用程序编程接口 (API) 以编程方式访问 PANTHER 工具和数据的可用服务。其他改进包括额外的植物基因组和更新的 PANTHER GO-slim。我们还扩展了通过应用程序编程接口 (API) 以编程方式访问 PANTHER 工具和数据的可用服务。其他改进包括额外的植物基因组和更新的 PANTHER GO-slim。我们还扩展了通过应用程序编程接口 (API) 以编程方式访问 PANTHER 工具和数据的可用服务。其他改进包括额外的植物基因组和更新的 PANTHER GO-slim。