NMPdb: Database of Nuclear Matrix Proteins.
NMPdb: Database of Nuclear Matrix Proteins.
复制标题
DOI：
10.1093/nar/gki132
复制
发表时间：
2005-01-01
影响因子：
14.9
通讯作者：
Rost B
中科院分区：
文献类型：
--
作者：
Mika S;Rost B
核基质（NM）是由蛋白质和RNA在真核细胞的核中聚集而产生的结构;它是在积极的DNA酶消化和盐提取方案之后保留的“粘性位”。由于NM在DNA复制、DNA转录和RNA剪接中的重要作用，NM蛋白的表达模式已成为许多癌症/肿瘤的重要早期指标。最近对NM结构的描述区分了网络状的“内部核基质”（INM）和将INM连接到内外核膜的“核壳”。一个谨慎的NM制备方案揭示了在INM顶部的蛋白质外壳;这些蛋白质通常被称为“核基质相关蛋白”。在这里，我们描述了一个新的数据库（NMPdb在http：//www.rostlab.org/db/NMPdb/），目前包含398 NM蛋白质的细节。我们通过对PubMed中3000多篇科学文章进行半自动分析来收集这些数据。我们可以将这398个蛋白质与UniProt或GenBank中的302个蛋白质序列进行匹配。我们的NMPdb存储库沿着以下注释注释这些链接：生物体、细胞类型、PubMed标识符、结构和功能特征的基于序列的预测，以及某些条目中负责定位的明确序列片段（核基质靶向信号）。
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).