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

@article{Mi2005, abstract = {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 approximately 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.}, author = {Mi, Huaiyu and Ulitsky, Betty L. and Loo, Rozina and Kejariwal, Anish and Vandergriff, Jody and Rabkin, Steven and Guo, Nan and Muruganujan, Anushya and Doremieux, Olivier and Campbell, Michael J. and Kitano, Hiroaki and Thomas, Paul D. }, citeulike-article-id = {2053696}, doi = {10.1093/nar/gki078}, journal = {Nucleic Acids Res}, keywords = {article-nar, article-pka-pkg, database, interface, panther, user-computer}, month = {Jan}, number = {Database issue}, pages = {D284--D288}, posted-at = {2007-12-04 01:53:38}, priority = {2}, title = {The {PANTHER} database of protein families, subfamilies, functions and pathways.}, volume = {33}, year = {2005} }

TY - JOUR ID - Mi2005 L3 - citeulike-article-id:2053696 TI - The {PANTHER} database of protein families, subfamilies, functions and pathways. JF - Nucleic Acids Res VL - 33 IS - Database issue SP - D284 EP - D288 N2 - 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 approximately 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. KW - article-nar KW - article-pka-pkg KW - database KW - interface KW - panther KW - user-computer AU - Mi, Huaiyu AU - Ulitsky, Betty AU - Loo, Rozina AU - Kejariwal, Anish AU - Vandergriff, Jody AU - Rabkin, Steven AU - Guo, Nan AU - Muruganujan, Anushya AU - Doremieux, Olivier AU - Campbell, Michael AU - Kitano, Hiroaki AU - Thomas, Paul PY - 2005/Jan// ER -