PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.
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DOI：
10.1093/nar/gkaa1106
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发表时间：
2021-01-08
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;Ebert D;Muruganujan A;Mills C;Albou LP;Mushayamaha T;Thomas PD
黑豹(通过进化关系进行蛋白质分析，http://www.pantherdb.org)是对生命所有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个系统发育树的文库，功能分类包括基因本体论术语和途径。在这里，我们分析目前来自不同分类组基因组的基因覆盖范围，以便用户在使用Panther工具分析基因列表时更好地了解预期的情况。我们还描述了在过去两年中对Panther所做的广泛改进。黑豹蛋白质类本体已经完全重构，6101个黑豹家族被手动分配到一个蛋白质类，提供了对蛋白质家族及其基因的高水平分类。用户可以访问TreeGrafter工具，将他们自己的蛋白质序列添加到黑豹的参考系统发育树中，以推断进化背景以及细粒度的注释。我们已经添加了人类增强子-基因链接，将非编码区与黑豹的注释人类基因联系在一起。我们还扩展了通过应用程序编程接口(API)对Panther工具和数据进行编程访问的可用服务。其他改进包括增加植物基因组和更新的Panther Go-Slim。
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.
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影响因子：
14.9
作者：
Mitchell AL;Attwood TK;Babbitt PC;Blum M;Bork P;Bridge A;Brown SD;Chang HY;El-Gebali S;Fraser MI;Gough J;Haft DR;Huang H;Letunic I;Lopez R;Luciani A;Madeira F;Marchler-Bauer A;Mi H;Natale DA;Necci M;Nuka G;Orengo C;Pandurangan AP;Paysan-Lafosse T;Pesseat S;Potter SC;Qureshi MA;Rawlings ND;Redaschi N;Richardson LJ;Rivoire C;Salazar GA;Sangrador-Vegas A;Sigrist CJA;Sillitoe I;Sutton GG;Thanki N;Thomas PD;Tosatto SCE;Yong SY;Finn RD
通讯作者：
Finn RD
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
DOI：
10.1093/database/bar068
发表时间：
2012
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Burge S;Kelly E;Lonsdale D;Mutowo-Muellenet P;McAnulla C;Mitchell A;Sangrador-Vegas A;Yong SY;Mulder N;Hunter S
通讯作者：
Hunter S
影响因子：
14.9
作者：
Wingender E;Schoeps T;Haubrock M;Krull M;Dönitz J
通讯作者：
Dönitz J
DOI：
10.1093/database/baw155
发表时间：
2016-12-26
影响因子：
5.8
作者：
Feuermann, Marc;Gaudet, Pascale;Thomas, Paul D.
通讯作者：
Thomas, Paul D.