title: Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
abstract: The vast amount of protein sequence data now available, together with accumulating experimental knowledge of protein function, enables modeling of protein sequence and function evolution. The PANTHER database was designed to model evolutionary sequence-function relationships on a large scale. There are a number of applications for these data, and we have implemented web services that address three of them. The first is a protein classification service. Proteins can be classified, using only their amino acid sequences, to evolutionary groups at both the family and subfamily levels. Specific subfamilies, and often families, are further classified when possible according to their functions, including molecular function and the biological processes and pathways they participate in. The second application, then, is an expression data analysis service, where functional classification information can help find biological patterns in the data obtained from genome-wide experiments. The third application is a coding single-nucleotide polymorphism scoring service. In this case, information about evolutionarily related proteins is used to assess the likelihood of a deleterious effect on protein function arising from a single substitution at a specific amino acid position in the protein. All three web services are available at http://www.pantherdb.org/tools.
authors.affiliation: Evolutionary Systems Biology Group, SRI International 333 Ravenswood Ave., Menlo Park CA 94025, USA paul.thomas@sri.com
authors.forename: Paul D
authors.initials: PD
authors.lastname: Thomas
authors.forename: Anish
authors.initials: A
authors.lastname: Kejariwal
authors.forename: Nan
authors.initials: N
authors.lastname: Guo
authors.forename: Huaiyu
authors.initials: H
authors.lastname: Mi
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Campbell
authors.forename: Anushya
authors.initials: A
authors.lastname: Muruganujan
authors.forename: Betty
authors.initials: B
authors.lastname: Lazareva-Ulitsky
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D003196:Computer Graphics; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D004331:Drosophila melanogaster / Q000235:genetics; D019143:Evolution, Molecular; D023281:Genomics; D006801:Humans; D020407:Internet; D008390:Markov Chains; D051379:Mice; D020641:Polymorphism, Single Nucleotide; D011506:Proteins / Q000145:classification / Q000235:genetics* / Q000502:physiology*; D012333:RNA, Messenger / Q000378:metabolism; D051381:Rats; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins; D012333:RNA, Messenger