ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins
ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins
复制标题
ENPD - 真核核酸结合蛋白数据库：将基因调控与蛋白质联系起来。
DOI：
10.1093/nar/gky1112
复制
发表时间：
2019-01-08
影响因子：
14.9
通讯作者：
Qin, Jing
中科院分区：
文献类型：
--
作者：
Leung, Ricky Wai Tak;Jiang, Xiaosen;Qin, Jing
真核细胞核酸结合蛋白数据库(ENPD，http://qinlab.sls.cuhk.edu.hk/ENPD/))是一个包含核酸结合蛋白及其功能信息的文库。DNA结合蛋白(DBPs)、RNA结合蛋白(RBPs)、DNA和RNA结合蛋白(DRBPs)等NBP通过与DNA和RNA的相互作用参与基因调控的各个阶段。由于nbps的重要性，该数据库是在人工整理和新开发的利用已测序转录本和基因组的管道的基础上建立的。该数据库总共记录了来自662个NBP科2423个物种的280万个NBP及其结合基序，构成了最大的NBP数据库。ENPD涵盖了进化上重要的谱系，这些谱系从未包括在以前的NBP数据库中，同时也发现了谱系特有的NBP家族扩展。ENPD还重点研究了DBPs、RBPs和DRBPs在非编码RNA(NcRNA)介导的基因调控中的作用。预测和实验验证的nbps靶点都已经在ENPD中被记录和手动管理，将ncRNAs、DNA调控元件和nbps之间的相互作用联系在基因调控中。该数据库为科学界提供了关键资源，为未来从功能和进化角度进行基因调控研究奠定了坚实的基础。
Eukaryotic nucleic acid binding protein database (ENPD, http://qinlab.sls.cuhk.edu.hk/ENPD/) is a library of nucleic acid binding proteins (NBPs) and their functional information. NBPs such as DNA binding proteins (DBPs), RNA binding proteins (RBPs), and DNA and RNA binding proteins (DRBPs) are involved in every stage of gene regulation through their interactions with DNA and RNA. Due to the importance of NBPs, the database was constructed based on manual curation and a newly developed pipeline utilizing both sequenced transcriptomes and genomes. In total the database has recorded 2.8 million of NBPs and their binding motifs from 662 NBP families and 2423 species, constituting the largest NBP database. ENPD covers evolutionarily important lineages which have never been included in the previous NBP databases, while lineage-specific NBP family expansions were also found. ENPD also focuses on the involvements of DBPs, RBPs and DRBPs in non-coding RNA (ncRNA) mediated gene regulation. The predicted and experimentally validated targets of NBPs have both been recorded and manually curated in ENPD, linking the interactions between ncRNAs, DNA regulatory elements and NBPs in gene regulation. This database provides key resources for the scientific community, laying a solid foundation for future gene regulatory studies from both functional and evolutionary perspectives.