Nucleic Acids Research, 2005, Vol. 33, Database issue D284-D288
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
The PANTHER database of protein families, subfamilies, functions and pathways
Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA and 1 The Systems Biology Institute and ERATO-SORST Kitano Symbiotic Systems Project/Japan Science and Technology Agency, Suite 6A, M31, 6-31-15 Jingumae, Shibuya, Tokyo 150-0001, Japan
* To whom correspondence should be addressed. Tel: +1 650 554 2723; Fax: +1 650 554 2344; Email: paul.thomas{at}appliedbiosystems.com
Received September 15, 2004; Revised and Accepted October 8, 2004
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.
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