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1.
Science 2004 Jan 23; 5657(303):540-3.
A map of the interactome network of the metazoan C. elegans.
Li S ,Armstrong CM ,Bertin N ,Ge H ,Milstein S ,Boxem M ,Vidalain PO ,Han JD ,Chesneau A ,Hao T ,Goldberg DS ,Li N ,Martinez M ,Rual JF ,Lamesch P ,Xu L ,Tewari M ,Wong SL ,Zhang LV ,Berriz GF ,Jacotot L ,Vaglio P ,Reboul J ,Hirozane-Kishikawa T ,Li Q ,Gabel HW ,Elewa A ,Baumgartner B ,Rose DJ ,Yu H ,Bosak S ,Sequerra R ,Fraser A ,Mango SE ,Saxton WM ,Strome S ,Van Den Heuvel S ,Piano F ,Vandenhaute J ,Sardet C ,Gerstein M ,Doucette-Stamm L ,Gunsalus KC ,Harper JW ,Cusick ME ,Roth FP ,Hill DE ,Vidal M ,
Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA.
To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with a subset of metazoan-specific proteins, more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens. Independent coaffinity purification assays experimentally validated the overall quality of this Y2H data set. Together with already described Y2H interactions and interologs predicted in silico, the current version of the Worm Interactome (WI5) map contains approximately 5500 interactions. Topological and biological features of this interactome network, as well as its integration with phenome and transcriptome data sets, lead to numerous biological hypotheses.
Publication Type: Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.;
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2.
Genome Res 2003 Apr ; 4(13):662-72.
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.
Camon E ,Magrane M ,Barrell D ,Binns D ,Fleischmann W ,Kersey P ,Mulder N ,Oinn T ,Maslen J ,Cox A ,Apweiler R ,
EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
Gene Ontology Annotation (GOA) is a project run by the European Bioinformatics Institute (EBI) that aims to provide assignments of terms from the Gene Ontology (GO) resource to gene products in a number of its databases (http://www.ebi.ac.uk/GOA). In the first stage of this project, GO assignments have been applied to a data set representing the complete human proteome by a combination of electronic mappings and manual curation. This vocabulary has also been applied to the nonredundant proteome sets for all other completely sequenced organisms as well as to proteins from a wide range of organisms where the proteome is not yet complete.
Publication Type: Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.;
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3.
Nucleic Acids Res 2003 Jan 1; 1(31):315-8.
The InterPro Database, 2003 brings increased coverage and new features.
Mulder NJ ,Apweiler R ,Attwood TK ,Bairoch A ,Barrell D ,Bateman A ,Binns D ,Biswas M ,Bradley P ,Bork P ,Bucher P ,Copley RR ,Courcelle E ,Das U ,Durbin R ,Falquet L ,Fleischmann W ,Griffiths-Jones S ,Haft D ,Harte N ,Hulo N ,Kahn D ,Kanapin A ,Krestyaninova M ,Lopez R ,Letunic I ,Lonsdale D ,Silventoinen V ,Orchard SE ,Pagni M ,Peyruc D ,Ponting CP ,Selengut JD ,Servant F ,Sigrist CJ ,Vaughan R ,Zdobnov EM ,
EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. mulder@ebi.ac.uk
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive resource. PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manually integrated and curated and are available in InterPro for text- and sequence-based searching. The results are provided in a single format that rationalises the results that would be obtained by searching the member databases individually. The latest release of InterPro contains 5629 entries describing 4280 families, 1239 domains, 95 repeats and 15 post-translational modifications. Currently, the combined signatures in InterPro cover more than 74% of all proteins in SWISS-PROT and TrEMBL, an increase of nearly 15% since the inception of InterPro. New features of the database include improved searching capabilities and enhanced graphical user interfaces for visualisation of the data. The database is available via a webserver (http://www.ebi.ac.uk/interpro) and anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).
Publication Type: Research Support, Non-U.S. Gov't;
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