title: PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.
abstract: The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators have associated the ontology terms with groups of protein sequences rather than individual sequences. Statistical models (Hidden Markov Models, or HMMs) are built from each of these groups. The advantage of this approach is that new sequences can be automatically classified as they become available. To ensure accurate functional classification, HMMs are constructed not only for families, but also for functionally distinct subfamilies. Multiple sequence alignments and phylogenetic trees, including curator-assigned information, are available for each family. The current version of the PANTHER database includes training sequences from all organisms in the GenBank non-redundant protein database, and the HMMs have been used to classify gene products across the entire genomes of human, and Drosophila melanogaster. The ontology terms and protein families and subfamilies, as well as Drosophila gene c;assifications, can be browsed and searched for free. Due to outstanding contractual obligations, access to human gene classifications and to protein family trees and multiple sequence alignments will temporarily require a nominal registration fee. PANTHER is publicly available on the web at http://panther.celera.com.
authors.affiliation: Protein Informatics, Celera Genomics, 850 Lincoln Center Drive, Foster City, CA 94404, USA. paul.thomas@fc.celera.com
authors.forename: Paul D
authors.initials: PD
authors.lastname: Thomas
authors.forename: Anish
authors.initials: A
authors.lastname: Kejariwal
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Campbell
authors.forename: Huaiyu
authors.initials: H
authors.lastname: Mi
authors.forename: Karen
authors.initials: K
authors.lastname: Diemer
authors.forename: Nan
authors.initials: N
authors.lastname: Guo
authors.forename: Istvan
authors.initials: I
authors.lastname: Ladunga
authors.forename: Betty
authors.initials: B
authors.lastname: Ulitsky-Lazareva
authors.forename: Anushya
authors.initials: A
authors.lastname: Muruganujan
authors.forename: Steven
authors.initials: S
authors.lastname: Rabkin
authors.forename: Jody A
authors.initials: JA
authors.lastname: Vandergriff
authors.forename: Olivier
authors.initials: O
authors.lastname: Doremieux
mesh_terms: D000818:Animals; D030562:Databases, Protein; D006801:Humans; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics / Q000502:physiology*; D016415:Sequence Alignment
chemical_list: D011506:Proteins