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Title | NMPdb: Database of Nuclear Matrix Proteins. |
Publication Type | Journal Article |
Year of Publication | 2005 |
Authors | Mika, S, Rost, B |
Journal | Nucleic Acids Res |
Volume | 33 |
Issue | Database issue |
Pagination | D160-3 |
Date Published | 2005 Jan 1 |
ISSN | 1362-4962 |
Keywords | Amino Acid Sequence, Animals, Databases, Protein, Humans, Mice, Nuclear Matrix-Associated Proteins, Rats |
Abstract | The nuclear matrix (NM) is a structure resulting from the aggregation of proteins and RNA in the nucleus of eukaryotic cells; it is the 'sticky bit' that remains after aggressive DNAse digestion and salt extraction protocols. Owing to the important role of the NM in DNA replication, DNA transcription and RNA splicing, the expression pattern of NM proteins has become an important early indicator for numerous cancers/tumors. Recent descriptions of the NM structure distinguish between a network-like 'internal nuclear matrix' (INM) and a 'nuclear shell' that connects the INM to the inner and outer nuclear membranes. A cautious NM preparation protocol reveals a coat of proteins on top of the INM; these proteins are usually referred to as the 'nuclear matrix-associated proteins'. Here, we describe a new database (NMPdb at http://www.rostlab.org/db/NMPdb/) that currently contains details of 398 NM proteins. We collected these data through a semi-automated analysis of over 3000 scientific articles in PubMed. We could match these 398 proteins to 302 protein sequences in UniProt or GenBank. Our NMPdb repository annotates these links along with the following annotations: organism, cell type, PubMed identifier, sequence-based predictions of structural and functional features and for some entries the explicit sequence segment that is responsible for localization (nuclear matrix targeting signal). |
DOI | 10.1093/nar/gki132 |
Alternate Journal | Nucleic Acids Res. |
PubMed ID | 15608168 |
PubMed Central ID | PMC540086 |
Grant List | R01-GM63029-01 / GM / NIGMS NIH HHS / United States R01-LM07329-01 / LM / NLM NIH HHS / United States |