Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools

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...

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Vydáno v:Nucleic acids research Ročník 34; číslo suppl-2; s. W645 - W650
Hlavní autoři: Thomas, Paul D., Kejariwal, Anish, Guo, Nan, Mi, Huaiyu, Campbell, Michael J., Muruganujan, Anushya, Lazareva-Ulitsky, Betty
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 01.07.2006
Témata:
Amino Acid Substitution
Animals
Computer Graphics
Data Interpretation, Statistical
Databases, Protein
Drosophila melanogaster - genetics
Evolution, Molecular
Genomics
Humans
Internet
Markov Chains
Mice
Polymorphism, Single Nucleotide
Proteins - classification
Proteins - genetics
Proteins - physiology
Rats
RNA, Messenger - metabolism
Sequence Analysis, Protein
Software
User-Computer Interface
ISSN:0305-1048, 1362-4962, 1362-4962
On-line přístup:Získat plný text
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Popis
Shrnutí: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.
Bibliografie:local:gkl229
To whom correspondence should be addressed. Tel: +1 650 859 2434; Fax: +1 650 859 3735; Email: paul.thomas@sri.com
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkl229