EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Issue 1 (2nd February 2020)

• Record Type: Journal Article
• Authors: Lin, Shaofeng; Wang, Chenwei; Zhou, Jiaqi; Shi, Ying; Ruan, Chen; Tu, Yiran; Yao, Lan; Peng, Di; Xue, Yu
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 1(2021)
• Page Start: 298
• Page End: 307
• Publication Date: 2020-02-02
• Subjects: phosphorylation -- phosphorylation site -- post-translational modification -- phosphoproteomics -- PLK1; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbz169
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: As an important post-translational modification (PTM), protein phosphorylation is involved in the regulation of almost all of biological processes in eukaryotes. Due to the rapid progress in mass spectrometry-based phosphoproteomics, a large number of phosphorylation sites (p-sites) have been characterized but remain to be curated. Here, we briefly summarized the current progresses in the development of data resources for the collection, curation, integration and annotation of p-sites in eukaryotic proteins. Also, we designed the eukaryotic phosphorylation site database (EPSD), which contained 1 616 804 experimentally identified p-sites in 209 326 phosphoproteins from 68 eukaryotic species. In EPSD, we not only collected 1 451 629 newly identified p-sites from high-throughput (HTP) phosphoproteomic studies, but also integrated known p-sites from 13 additional databases. Moreover, we carefully annotated the phosphoproteins and p-sites of eight model organisms by integrating the knowledge from 100 additional resources that covered 15 aspects, including phosphorylation regulator, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, protein expression/proteomics and subcellular localization. We anticipate that the EPSD can serve as a useful resource for further analysis of eukaryotic phosphorylation. With a data volume of 14.1 GB, EPSD is free for all users at http://epsd.biocuckoo.cn/ .