NAR Molecular Biology Database Collection entry number 1267
Alves-Cruzeiro, J., Nogales-Cadenas, R., Pascual-Montano, A.
Functional Bioinformatics Group. National Center for Biotechnology-CSIC. Madrid, Spain
We present the second generation of centrosomeDB, available online at http://centrosome.cnb.csic.es, with a significant expansion of 1357 human and drosophila centrosomal genes and their corresponding information. The centrosome of animal cells takes part in important biological processes such as the organization of the interphase microtubule cytoskeleton and the assembly of the mitotic spindle. The active research done during the past decades has produced lots of data related to centrosomal proteins. Unfortunately, the accumulated data is dispersed among diverse and heterogeneous sources of information. We believe that the availability of a repository collecting curated evidences of centrosomal proteins would constitute a key resource for the scientific community. This was our first motivation to introduce CentrosomeDB in NAR database issue in 2009, collecting a set of human centrosomal proteins that were reported in the literature and other sources. The intensive use of this resource during these years has encouraged us to present this new expanded version. Using our database, the researcher is offered the possibility to study the evolution, function, and structure of the centrosome. We have compiled information from many sources, including Gene Ontology, disease-association, single nucleotide polymorphisms, and associated gene expression experiments. Special interest has been paid to protein-protein interaction.
In this new version of CentrosomeDB the set of human centrosomal genes was significantly amplified to 1053, being a solid improvement against the 383 genes of the first version. In addition to this, we also collected 304 Drosophila melanogaster genes likely to be localized in the centrosome, which comes towards the â€œfuture perspectivesâ€ of the first version â€“ to widen the range of species of CentrosomeDB. There were also some changes in the way information can be treated, with the interactions becoming the focus of this new generation. In fact, our updated database allows the user to obtain the interactome of a set of any genes against the centrosomal genes, the genes located to the â€œnuclear membraneâ€ and the â€œGolgi apparatusâ€ and the genes involved in the cell-cycle progression like the CDK's and the cyclins. With this new version, the user can recreate any interaction's user case using the tools provided by CentrosomeDB exclusively, and make a full interactions centric study of any centrosomal gene in particular.
This work was supported by the Government of Madrid (CAM) [P2010/BMD-2305]; the Spanish Minister of Science and Innovation [BIO2010-17527]; and the Juan de la Cierva research program [to RNC]. Funding for open access charge: Government of Madrid (CAM).
Category: Protein sequence databases
Subcategory: Protein localization and targeting
Go to the abstract in the NAR 2014 Database Issue.
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