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NMPdb: Database of Nuclear Matrix Proteins.

Sven Mika1, Burkhard Rost

  • 1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA. mika@cubic.bioc.columbia.edu

Nucleic Acids Research
|December 21, 2004
PubMed
Summary

A new database, NMPdb, catalogs 398 nuclear matrix (NM) proteins involved in crucial cellular processes like DNA replication and transcription. This resource aids cancer research by tracking NM protein expression as an early tumor indicator.

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Area of Science:

  • Cell Biology
  • Bioinformatics
  • Proteomics

Background:

  • The nuclear matrix (NM) is a key nuclear structure involved in DNA replication, transcription, and RNA splicing.
  • NM protein expression patterns are significant early indicators for various cancers.
  • Recent research differentiates the internal nuclear matrix (INM) and nuclear shell structures.

Purpose of the Study:

  • To introduce NMPdb, a novel database detailing nuclear matrix proteins.
  • To consolidate information on NM proteins from scientific literature.
  • To provide a resource for studying NM proteins in cancer diagnostics.

Main Methods:

  • Semi-automated analysis of over 3000 PubMed articles.
  • Data compilation and curation for NM proteins.

Related Experiment Videos

  • Matching NM proteins to sequences in UniProt/GenBank.

    • Main Results:

    • NMPdb contains information on 398 NM proteins.
    • 302 of these proteins were matched to sequences in UniProt or GenBank.
    • The database includes annotations on organism, cell type, PubMed ID, predicted features, and nuclear matrix targeting signals.

    Conclusions:

    • NMPdb serves as a valuable resource for cancer research and cell biology studies.
    • The database facilitates the investigation of nuclear matrix proteins and their roles in disease.
    • NMPdb supports further research into nuclear matrix targeting signals and protein functions.