PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.
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DOI：
10.1093/nar/gkp1019
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发表时间：
2010-01
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;Dong Q;Muruganujan A;Gaudet P;Lewis S;Thomas PD
通过进化关系分析蛋白质（PANTHER）是一个综合性的软件系统，用于根据基因的进化关系推断基因的功能。基因家族的系统发育树构成了PANTHER的基础，这些树用本体术语注释，描述了基因功能从祖先到现代基因的进化。PANTHER的主要应用之一是基于未表征基因与实验中已知功能基因的进化关系，准确预测未表征基因的功能。PANTHER网站，可在http://www.pantherdb.org免费获得，还包括用于分析与已知和推断基因功能相关的基因组数据的软件工具。自2007年以来，PANTHER有几个新的发展：(i)改进的系统发育树，明确表示物种形成和基因复制事件；（ii）基因同源物的鉴定，包括最少分化的同源物（最佳一对一对）；（iii）更多基因组的覆盖范围(48个基因组，每个基因组中高达87%的基因；见http://www.pantherdb.org/panther/summaryStats.jsp), （iv）改进了对基因、蛋白质和微阵列探针的替代数据库标识符的支持，(v)采用了SBGN标准来显示生物途径。此外，作为基因本体论参考基因组计划的一部分，PANTHER树正在用基因功能进行注释，导致越来越多的策划功能注释。
Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website, freely available at http://www.pantherdb.org, also includes software tools for analyzing genomic data relative to known and inferred gene functions. Since 2007, there have been several new developments to PANTHER: (i) improved phylogenetic trees, explicitly representing speciation and gene duplication events, (ii) identification of gene orthologs, including least diverged orthologs (best one-to-one pairs), (iii) coverage of more genomes (48 genomes, up to 87% of genes in each genome; see http://www.pantherdb.org/panther/summaryStats.jsp), (iv) improved support for alternative database identifiers for genes, proteins and microarray probes and (v) adoption of the SBGN standard for display of biological pathways. In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resulting in an increasing number of curated functional annotations.
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拟南芥信息资源（TAIR）：基因结构和功能注释。
影响因子：
14.9
作者：
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影响因子：
4.3
作者：
Reference Genome Group of the Gene Ontology Consortium
通讯作者：
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影响因子：
14.9
作者：
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Mouse Genome Database Group
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
14.9
作者：
Sprague J;Bayraktaroglu L;Bradford Y;Conlin T;Dunn N;Fashena D;Frazer K;Haendel M;Howe DG;Knight J;Mani P;Moxon SA;Pich C;Ramachandran S;Schaper K;Segerdell E;Shao X;Singer A;Song P;Sprunger B;Van Slyke CE;Westerfield M
通讯作者：
Westerfield M