Analysing the yeast complexome-the Complex Portal rising to the challenge.

Datasets as Topic Gene Ontology Knowledge Bases Saccharomyces cerevisiae / genetics Saccharomyces cerevisiae Proteins / genetics

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
06 04 2021
Historique:
accepted: 27 01 2021
revised: 22 01 2021
received: 03 11 2020
pubmed: 8 3 2021
medline: 13 5 2021
entrez: 7 3 2021
Statut: ppublish

Résumé

The EMBL-EBI Complex Portal is a knowledgebase of macromolecular complexes providing persistent stable identifiers. Entries are linked to literature evidence and provide details of complex membership, function, structure and complex-specific Gene Ontology annotations. Data are freely available and downloadable in HUPO-PSI community standards and missing entries can be requested for curation. In collaboration with Saccharomyces Genome Database and UniProt, the yeast complexome, a compendium of all known heteromeric assemblies from the model organism Saccharomyces cerevisiae, was curated. This expansion of knowledge and scope has led to a 50% increase in curated complexes compared to the previously published dataset, CYC2008. The yeast complexome is used as a reference resource for the analysis of complexes from large-scale experiments. Our analysis showed that genes coding for proteins in complexes tend to have more genetic interactions, are co-expressed with more genes, are more multifunctional, localize more often in the nucleus, and are more often involved in nucleic acid-related metabolic processes and processes where large machineries are the predominant functional drivers. A comparison to genetic interactions showed that about 40% of expanded co-complex pairs also have genetic interactions, suggesting strong functional links between complex members.

Identifiants

DOI: 10.1093/nar/gkab077 PMID: 33677561 PMC: PMC8034636
pubmed: 33677561
pii: 6157094
doi: 10.1093/nar/gkab077
pmc: PMC8034636
doi:

Substances chimiques

Saccharomyces cerevisiae Proteins 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

3156-3167

Subventions

Organisme : Wellcome Trust
ID : 212925/Z/18/Z
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : U41 HG001315
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG002273
Pays : United States
Organisme : NHGRI NIH HHS
ID : U41 HG002223
Pays : United States
Organisme : NHGRI NIH HHS
ID : U24 HG007822
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom

Informations de copyright

© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Birgit H M Meldal (BHM)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Carles Pons (C)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, 08028 Barcelona, Catalonia, Spain.

Livia Perfetto (L)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Noemi Del-Toro (N)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Edith Wong (E)

Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA.

Patrick Aloy (P)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, 08028 Barcelona, Catalonia, Spain.
Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain.

Henning Hermjakob (H)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Sandra Orchard (S)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Pablo Porras (P)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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Classifications MeSH

questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Collecte de données › Jeux de données comme sujet › Analysing the yeast complexome-the Complex...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Vocabulaire contrôlé › Ontologies biologiques › Gene Ontology › Analysing the yeast complexome-the Complex...
questionsmedicales.fr › Sciences de l'information › Informatique › Informatique médicale › Applications de l'informatique médicale › Systèmes d'information › Bases de connaissances › Analysing the yeast complexome-the Complex...
questionsmedicales.fr › Eucaryotes › Champignons › Levures › Saccharomyces › Saccharomyces cerevisiae › Analysing the yeast complexome-the Complex...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines fongiques › Protéines de Saccharomyces cerevisiae › Analysing the yeast complexome-the Complex...