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Nucleic Acids Res. 2019 Jan 8;47(D1):D322-D329. doi: 10.1093/nar/gky1112.

ENPD - A Database of Eukaryotic Nucleic Acid Binding Proteins: Linking Gene Regulations to Proteins.

Tak Leung RW1, Jiang X2,3,4, Chu KH1,2, Qin J1,2,5.

Author information

1
School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China.
2
Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China.
3
School of Future Technology, The University of Chinese Academy of Sciences, Beijing 100049, China.
4
College of Life Science & Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
5
School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China.

Abstract

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.

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