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. 2003 Jan 1;31(1):328-30.
doi: 10.1093/nar/gkg018.

The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome

G Dellaire  1 , R Farrall, W A Bickmore
Affiliations

The Nuclear Protein Database (NPD): sub-nuclear localisation and functional annotation of the nuclear proteome

G Dellaire et al. Nucleic Acids Res. .

Abstract

The Nuclear Protein Database (NPD) is a curated database that contains information on more than 1300 vertebrate proteins that are thought, or are known, to localise to the cell nucleus. Each entry is annotated with information on predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. In addition, information on the sub-nuclear localisation of each protein is provided and the biological and molecular functions are described using Gene Ontology (GO) terms. The database is searchable by keyword, protein name, sub-nuclear compartment and protein domain/motif. Links to other databases are provided (e.g. Entrez, SWISS-PROT, OMIM, PubMed, PubMed Central). Thus, NPD provides a gateway through which the nuclear proteome may be explored. The database can be accessed at http://npd.hgu.mrc.ac.uk and is updated monthly.

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Figures

Figure 1
Figure 1
Overview of the Nuclear Protein Database (NPD). Data is entered into a dedicated MS Access database (triangle) and once a month the Access data tables are converted to MySQL tables using MS Visual Basic (VBA). The SQL tables are then copied to the external MySQL server (hexagon) to be queried using PHP (thick arrows). NPD can be searched using Boolean operators via the web using the main search page. Alternately, the database may be queried by compartment (Compartment Browser) or protein domain (Domain Browser). Search results (dashed arrows) are returned as a meta-list of matching gene entries. The individual entries are retrieved by clicking on the main gene name, which queries the MySQL server once again returning a protein data sheet (PDS) containing archived and external database information. All result and PDS web pages are generated dynamically using PHP. Web pages are represented by squares.
Figure 2
Figure 2
The NPD Compartment Browser. The compartment browser (A) provides an overview of each of the principal sub-nuclear compartments. Upon selecting a compartment (i.e. PML) an overview page (B) is generated with an image of that compartment and a short abstract describing its structure, function and relevance to human disease. Links to external Internet resources are also provided. In addition, the NPD can be searched for proteins associated with a given domain (C) from the overview page (i.e. BLM, Bright and CBP are returned for PML bodies). Nucleus illustration reproduced by permission of Dr David L. Spector, Cold Spring Harbor Laboratory.
See this image and copyright information in PMC

References

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