Web of Science: 6 cites, Scopus: 8 cites, Google Scholar: cites
Gene ontology function prediction in Mollicutes using protein-protein association networks
Gómez, Antonio (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Cedano Rodríguez, Juan Antonio (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Amela, Isaac (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Planas, Antoni (Institut Químic de Sarrià)
Piñol Ribas, Jaume (Universitat Autònoma de Barcelona. Departament de Bioquímica i Biologia Molecular)
Querol Murillo, Enrique (Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")

Data: 2011
Resum: Many complex systems can be represented and analysed as networks. The recent availability of large-scale datasets, has made it possible to elucidate some of the organisational principles and rules that govern their function, robustness and evolution. However, one of the main limitations in using protein-protein interactions for function prediction is the availability of interaction data, especially for Mollicutes. If we could harness predicted interactions, such as those from a Protein-Protein Association Networks (PPAN), combining several protein-protein network function-inference methods with semantic similarity calculations, the use of protein-protein interactions for functional inference in this species would become more potentially useful. In this work we show that using PPAN data combined with other approximations, such as functional module detection, orthology exploitation methods and Gene Ontology (GO)-based information measures helps to predict protein function in Mycoplasma genitalium. To our knowledge, the proposed method is the first that combines functional module detection among species, exploiting an orthology procedure and using information theory-based GO semantic similarity in PPAN of the Mycoplasma species. The results of an evaluation show a higher recall than previously reported methods that focused on only one organism network.
Nota: Número d'acord de subvenció MCYT/BFU2010-22209-C02
Nota: Número d'acord de subvenció MCYT/BIO2007-67904-C02
Drets: Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original. Creative Commons
Llengua: Anglès.
Document: article ; recerca ; publishedVersion
Publicat a: BMC systems biology, Vol. 5 (April 2011) , art. 49, ISSN 1752-0509

PMID: 21486441
DOI: 10.1186/1752-0509-5-49


11 p, 1.3 MB

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