PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.
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DOI：
10.1093/nar/gkw1138
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发表时间：
2017-01-04
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;Huang X;Muruganujan A;Tang H;Mills C;Kang D;Thomas PD
PANTHER数据库（Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org）包含来自104个完全测序的基因组的蛋白质编码基因的进化和功能的全面信息。PANTHER软件工具允许用户对新的蛋白质序列进行分类，并分析从大规模基因组学实验中获得的基因列表。在过去的一年中，主要的改进包括PANTHER中可用分类信息的大量扩展，以及对分析工具的重大增强。由于基因本体系统发育注释项目的进展，蛋白质亚家族功能分类增加了一倍多。对于人类基因（以及其他一些生物），PANTHER现在也支持使用来自Reactome资源的途径分类进行富集分析。基因列表富集工具包括一个新的结果“分层视图”，使用户能够利用分类/本体的结构；这些工具还允许用户直接上传基因变异数据，而不需要事先转换成基因列表。更新的编码单核苷酸多态性（SNP）评分工具使用改进的算法。隐马尔可夫模型（HMM）搜索工具现在使用HMMER3，大大减少了搜索时间，提高了e值统计的准确性。最后，PANTHER树属性查看器已经在JavaScript中实现，提供了探索蛋白质序列进化的新视图。
The PANTHER database (Protein ANalysis THrough Evolutionary Relationships, http://pantherdb.org) contains comprehensive information on the evolution and function of protein-coding genes from 104 completely sequenced genomes. PANTHER software tools allow users to classify new protein sequences, and to analyze gene lists obtained from large-scale genomics experiments. In the past year, major improvements include a large expansion of classification information available in PANTHER, as well as significant enhancements to the analysis tools. Protein subfamily functional classifications have more than doubled due to progress of the Gene Ontology Phylogenetic Annotation Project. For human genes (as well as a few other organisms), PANTHER now also supports enrichment analysis using pathway classifications from the Reactome resource. The gene list enrichment tools include a new ‘hierarchical view’ of results, enabling users to leverage the structure of the classifications/ontologies; the tools also allow users to upload genetic variant data directly, rather than requiring prior conversion to a gene list. The updated coding single-nucleotide polymorphisms (SNP) scoring tool uses an improved algorithm. The hidden Markov model (HMM) search tools now use HMMER3, dramatically reducing search times and improving accuracy of E-value statistics. Finally, the PANTHER Tree-Attribute Viewer has been implemented in JavaScript, with new views for exploring protein sequence evolution.
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影响因子：
14.9
作者：
Mitchell A;Chang HY;Daugherty L;Fraser M;Hunter S;Lopez R;McAnulla C;McMenamin C;Nuka G;Pesseat S;Sangrador-Vegas A;Scheremetjew M;Rato C;Yong SY;Bateman A;Punta M;Attwood TK;Sigrist CJ;Redaschi N;Rivoire C;Xenarios I;Kahn D;Guyot D;Bork P;Letunic I;Gough J;Oates M;Haft D;Huang H;Natale DA;Wu CH;Orengo C;Sillitoe I;Mi H;Thomas PD;Finn RD
通讯作者：
Finn RD
DOI：
10.1073/pnas.0404380101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Thomas, PD;Kejariwal, A
通讯作者：
Kejariwal, A
影响因子：
5.8
作者：
Mottaz, Anais;David, Fabrice P. A.;Yip, Yum L.
通讯作者：
Yip, Yum L.
影响因子：
14.9
作者：
Mi H;Poudel S;Muruganujan A;Casagrande JT;Thomas PD
通讯作者：
Thomas PD
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium