title: The PANTHER database of protein families, subfamilies, functions and pathways.
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.
authors.affiliation: Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA.
authors.forename: Huaiyu
authors.initials: H
authors.lastname: Mi
authors.forename: Betty
authors.initials: B
authors.lastname: Lazareva-Ulitsky
authors.forename: Rozina
authors.initials: R
authors.lastname: Loo
authors.forename: Anish
authors.initials: A
authors.lastname: Kejariwal
authors.forename: Jody
authors.initials: J
authors.lastname: Vandergriff
authors.forename: Steven
authors.initials: S
authors.lastname: Rabkin
authors.forename: Nan
authors.initials: N
authors.lastname: Guo
authors.forename: Anushya
authors.initials: A
authors.lastname: Muruganujan
authors.forename: Olivier
authors.initials: O
authors.lastname: Doremieux
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Campbell
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
authors.forename: Paul D
authors.initials: PD
authors.lastname: Thomas
mesh_terms: D000818:Animals; D030562:Databases, Protein / Q000706:statistics & numerical data; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D008390:Markov Chains; D051379:Mice; D011506:Proteins / Q000737:chemistry / Q000145:classification* / Q000502:physiology; D051381:Rats; D020539:Sequence Analysis, Protein; D015398:Signal Transduction; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D011506:Proteins