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Literature DB >> 12520037

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes.

Manuela Pruess¹, Wolfgang Fleischmann, Alexander Kanapin, Youla Karavidopoulou, Paul Kersey, Evgenia Kriventseva, Virginie Mittard, Nicola Mulder, Isabelle Phan, Florence Servant, Rolf Apweiler.

Abstract

The Proteome Analysis database (http://www.ebi.ac.uk/proteome/) has been developed by the Sequence Database Group at EBI utilizing existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes of bacteria, archeae and eukaryotes. Three main projects are used, InterPro, CluSTr and GO Slim, to give an overview on families, domains, sites, and functions of the proteins from each of the complete genomes. Complete proteome analysis is available for a total of 89 proteome sets. A specifically designed application enables InterPro proteome comparisons for any one proteome against any other one or more of the proteomes in the database.

Entities: Gene

Mesh：

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Year: 2003 PMID： 12520037 PMCID： PMC165552 DOI： 10.1093/nar/gkg105

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

11 in total

1. The Protein Data Bank.

Authors: H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. The InterPro database, an integrated documentation resource for protein families, domains and functional sites.

Authors: R Apweiler; T K Attwood; A Bairoch; A Bateman; E Birney; M Biswas; P Bucher; L Cerutti; F Corpet; M D Croning; R Durbin; L Falquet; W Fleischmann; J Gouzy; H Hermjakob; N Hulo; I Jonassen; D Kahn; A Kanapin; Y Karavidopoulou; R Lopez; B Marx; N J Mulder; T M Oinn; M Pagni; F Servant; C J Sigrist; E M Zdobnov
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

3. CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.

Authors: E V Kriventseva; W Fleischmann; E M Zdobnov; R Apweiler
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

4. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors: M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal: Nat Genet Date: 2000-05 Impact factor: 38.330

5. SCOP database in 2002: refinements accommodate structural genomics.

Authors: Loredana Lo Conte; Steven E Brenner; Tim J P Hubbard; Cyrus Chothia; Alexey G Murzin
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

6. The EMBL Nucleotide Sequence Database.

Authors: Guenter Stoesser; Wendy Baker; Alexandra van den Broek; Evelyn Camon; Maria Garcia-Pastor; Carola Kanz; Tamara Kulikova; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Nicole Redaschi; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

7. The Ensembl genome database project.

Authors: T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

8. Interactive InterPro-based comparisons of proteins in whole genomes.

Authors: A Kanapin; R Apweiler; M Biswas; W Fleischmann; Y Karavidopoulou; P Kersey; E V Kriventseva; V Mittard; N Mulder; T Oinn; I Phan; F Servant; E Zdobnov
Journal: Bioinformatics Date: 2002-02 Impact factor: 6.937

9. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

Authors: A Bairoch; R Apweiler
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

10. Protein folds and families: sequence and structure alignments.

Authors: L Holm; C Sander
Journal: Nucleic Acids Res Date: 1999-01-01 Impact factor: 16.971

22 in total

1. Phylogenetic analysis of Sec7-domain-containing Arf nucleotide exchangers.

Authors: Randal Cox; Roberta J Mason-Gamer; Catherine L Jackson; Nava Segev
Journal: Mol Biol Cell Date: 2004-01-23 Impact factor: 4.138

2. TrSDB: a proteome database of transcription factors.

Authors: Antoni Hermoso; Daniel Aguilar; Francesc X Aviles; Enrique Querol
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

3. The EMBL Nucleotide Sequence Database.

Authors: Tamara Kulikova; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Kirsty Bates; Paul Browne; Alexandra van den Broek; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Maria Garcia-Pastor; Nicola Harte; Carola Kanz; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle McHale; Francesco Nardone; Ville Silventoinen; Peter Stoehr; Guenter Stoesser; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

10. Quantitative screening of advanced glycation endproducts in cellular and extracellular proteins by tandem mass spectrometry.

Authors: Paul J Thornalley; Sinan Battah; Naila Ahmed; Nikolaos Karachalias; Stamatina Agalou; Roya Babaei-Jadidi; Anne Dawnay
Journal: Biochem J Date: 2003-11-01 Impact factor: 3.857