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Nucleic Acids Research 2006 34(Database Issue):D218-D220; doi:10.1093/nar/gkj004
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Nucleic Acids Research, 2006, Vol. 34, Database issue D218-D220
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

NOPdb: Nucleolar Proteome Database

Anthony Kar Lun Leung*, Laura Trinkle-Mulcahy, Yun Wah Lam, Jens S. Andersen1, Matthias Mann1 and Angus I. Lamond

Division of Gene Regulation and Expression, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee Dundee DD1 5EH, UK 1Department of Biochemistry and Molecular Biology, University of Southern Denmark Campusvej 55, DK-5230 Odense M, Denmark

*To whom correspondence should be addressed. Tel: +1 617 253 0265; Fax: +1 617 253 3867; Email: akleung{at}mit.edu

Received August 13, 2005. Accepted August 16, 2005.

The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain structures and relevant protein homologues across species, as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of ~500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints, highlighted by visualization means in the NOPdb, provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/uncharacterized proteins. The NOPdb (http://www.lamondlab.com/NOPdb) is searchable by either gene names, nucleotide or protein sequences, Gene Ontology terms or motifs, or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink, OMIM and PubMed).

Present address: Anthony K. L. Leung, Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA


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