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NOPdb: Nucleolar Proteome Database


NAR Molecular Biology Database Collection entry number 706
Leung A.K.1, Trinkle-Mulcahy L2. and Lamond, A.I.2
1Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
2School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, Scotland, UK
Contact akleung@mit.edu

Database Description

The Nucleolar Proteome Database (NOPdb) archives data on more than 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, 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).

Recent Developments

The database is currently also searchable by mRNA sequences or by short amino acid sequences. Moreover, we planned to include an online-documentation to help users to surf through the site and additional kinetic profiles for each protein, based on their responses to both different drug treatments and other metabolic and cell cycle variations.

Acknowledgements

The Human Frontier Science Program is acknowledged for a research grant entitled 'Functional organization of the cell nucleus investigated through proteomics and molecular dynamics’. We thank many colleagues working diligently to explore the dynamic nucleolar proteome in the ongoing collaboration between the laboratories of Angus I Lamond (University of Dundee) and Matthias Mann (University of Southern Denmark)

References

1. Andersen, J.S., Lyon, C.E., Fox, A.H., Leung, A.K., Lam, Y.W., Steen, H., Mann, M. and Lamond, A.I. (2002) Directed proteomic analysis of the human nucleolus. Curr Biol, 12, 1-11.
2.Leung, A.K., Andersen, J.S., Mann, M. and Lamond, A.I. (2003) Bioinformatic analysis of the nucleolus. Biochem J, 376, 553-569.


Go to the abstract in the NAR 2006 Database Issue.
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