Large-scale gene function analysis with the PANTHER classification system.
Large-scale gene function analysis with the PANTHER classification system.
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DOI：
10.1038/nprot.2013.092
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发表时间：
2013-08
期刊：
影响因子：
14.8
通讯作者：
Thomas PD
中科院分区：
文献类型：
--
作者：
Mi H;Muruganujan A;Casagrande JT;Thomas PD
PANTHER分类系统（www.pantherdb.org）是一个综合系统，它结合了基因功能、本体、途径和统计分析工具，使生物学家能够分析大规模的全基因组实验数据。该系统由82个完整的基因组组成，分为基因家族和亚家族，它们的进化关系在系统发育树、多序列比对和统计模型（隐藏马尔可夫模型或HISTORY）中被捕获。基因按其功能以几种不同的方式分类：家族和亚家族用本体论术语（基因本体论和PANTHER蛋白类）注释，序列被分配到PANTHER途径。PANTHER网站包括一套工具，允许用户浏览和查询基因功能，并通过一些统计测试分析大规模实验数据。它被实验室科学家、生物信息学家、计算机科学家和系统生物学家广泛使用。在2013年发布的PANTHER（v.8.0）中，除了更新数据内容外，还重新设计了网站界面，以改善用户体验和分析能力。本方案将详细描述如何在PANTHER分类系统中分析全基因组实验数据。
PANTHER Classification System (www.pantherdb.org) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools to enable biologists to analyze large-scale genome-wide experimental data. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (Hidden-Markov Models, or HMMs). Genes are classified by their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology and PANTHER Protein Class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools to allow users to browse and query gene functions, and analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), besides the update of the data content, the website interface was redesigned to improve the user experience and analytical capability. This protocol will provide a detailed description of how to analyze genome-wide experimental data in the PANTHER Classification System.
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基因本体论：2011年的增强。
影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
10.6
作者：
Hek, Karin;Demirkan, Ayse;Lahti, Jari;Terracciano, Antonio;Teumer, Alexander;Cornelis, Marilyn C.;Amin, Najaf;Bakshis, Erin;Baumert, Jens;Ding, Jingzhong;Liu, Yongmei;Marciante, Kristin;Meirelles, Osorio;Nalls, Michael A.;Sun, Yan V.;Vogelzangs, Nicole;Yu, Lei;Bandinelli, Stefania;Benjamin, Emelia J.;Bennett, David A.;Boomsma, Dorret;Cannas, Alessandra;Coker, Laura H.;de Geus, Eco;De Jager, Philip L.;Diez-Roux, Ana V.;Purcell, Shaun;Hu, Frank B.;Rimm, Eric B.;Hunter, David J.;Jensen, Majken K.;Curhan, Gary;Rice, Kenneth;Penman, Alan D.;Rotter, Jerome I.;Sotoodehnia, Nona;Emeny, Rebecca;Eriksson, Johan G.;Evans, Denis A.;Ferrucci, Luigi;Fornage, Myriam;Gudnason, Vilmundur;Hofman, Albert;Illig, Thomas;Kardia, Sharon;Kelly-Hayes, Margaret;Koenen, Karestan;Kraft, Peter;Kuningas, Maris;Massaro, Joseph M.;Melzer, David;Mulas, Antonella;Mulder, Cornelis L.;Murray, Anna;Oostra, Ben A.;Palotie, Aarno;Penninx, Brenda;Petersmann, Astrid;Pilling, Luke C.;Psaty, Bruce;Rawal, Rajesh;Reiman, Eric M.;Schulz, Andrea;Shulman, Joshua M.;Singleton, Andrew B.;Smith, Albert V.;Sutin, Angelina R.;Uitterlinden, Andre G.;Voelzke, Henry;Widen, Elisabeth;Yaffe, Kristine;Zonderman, Alan B.;Cucca, Francesco;Harris, Tamara;Ladwig, Karl-Heinz;Llewellyn, David J.;Raikkonen, Katri;Tanaka, Toshiko;van Duijn, Cornelia M.;Grabe, Hans J.;Launer, Lenore J.;Lunetta, Kathryn L.;Mosley, Thomas H., Jr.;Newman, Anne B.;Tiemeier, Henning;Murabito, Joanne
通讯作者：
Murabito, Joanne
影响因子：
4.3
作者：
Reference Genome Group of the Gene Ontology Consortium
通讯作者：
Reference Genome Group of the Gene Ontology Consortium
Dnmt1 和 Dnmt3a 维持 DNA 甲基化并调节成人前脑神经元的突触功能
影响因子：
25
作者：
Feng, Jian;Zhou, Yu;Campbell, Susan L.;Le, Thuc;Li, En;Sweatt, J. David;Silva, Alcino J.;Fan, Guoping
通讯作者：
Fan, Guoping
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J