The PANTHER database of protein families, subfamilies, functions and pathways

PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (ontology terms and pathway...

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Bibliographic Details
Published in:	Nucleic acids research Vol. 33; no. suppl-1; pp. D284 - D288
Main Authors:	Mi, Huaiyu, Lazareva-Ulitsky, Betty, Loo, Rozina, Kejariwal, Anish, Vandergriff, Jody, Rabkin, Steven, Guo, Nan, Muruganujan, Anushya, Doremieux, Olivier, Campbell, Michael J., Kitano, Hiroaki, Thomas, Paul D.
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01-01-2005 Oxford Publishing Limited (England)
Subjects:	Animals Databases, Protein - statistics & numerical data Gene Expression Profiling Humans Internet Markov Chains Mice Proteins - chemistry Proteins - classification Proteins - physiology Rats Sequence Analysis, Protein Signal Transduction Systems Integration User-Computer Interface
Online Access:	Get full text
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Summary:	PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (ontology terms and pathways), as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. The latest version, 5.0, contains 6683 protein families, divided into 31 705 subfamilies, covering ∼90% of mammalian protein-coding genes. PANTHER 5.0 includes a number of significant improvements over previous versions, most notably (i) representation of pathways (primarily signaling pathways) and association with subfamilies and individual protein sequences; (ii) an improved methodology for defining the PANTHER families and subfamilies, and for building the HMMs; (iii) resources for scoring sequences against PANTHER HMMs both over the web and locally; and (iv) a number of new web resources to facilitate analysis of large gene lists, including data generated from high-throughput expression experiments. Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com.
Bibliography:	istex:D7F6CFD24DC4A0F21EB7FB0D54ED59A9B319AB25 ark:/67375/HXZ-C7449JZ7-9 local:gki078 To whom correspondence should be addressed. Tel: +1 650 554 2723; Fax: +1 650 554 2344; Email: paul.thomas@appliedbiosystems.com Received September 15, 2004; Revised and Accepted October 8, 2004 ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 2005, the authors The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions@oupjournals.org.
ISSN:	0305-1048 1362-4962 1362-4962
DOI:	10.1093/nar/gki078