Abstract
Here, we described the updated database iEKPD 2.0 (http://iekpd.biocuckoo.org) for eukaryotic protein kinases (PKs), protein phosphatases (PPs) and proteins containing phosphoprotein-binding domains (PPBDs), which are key molecules responsible for phosphorylation-dependent signalling networks and participate in the regulation of almost all biological processes and pathways. In total, iEKPD 2.0 contained 197 348 phosphorylation regulators, including 109 912 PKs, 23 294 PPs and 68 748 PPBD-containing proteins in 164 eukaryotic species. In particular, we provided rich annotations for the regulators of eight model organisms, especially humans, by compiling and integrating the knowledge from 100 widely used public databases that cover 13 aspects, including cancer mutations, genetic variations, disease-associated information, mRNA expression, DNA & RNA elements, DNA methylation, molecular interactions, drug-target relations, protein 3D structures, post-translational modifications, protein expressions/proteomics, subcellular localizations and protein functional annotations. Compared with our previously developed EKPD 1.0 (∼0.5 GB), iEKPD 2.0 contains ∼99.8 GB of data with an ∼200-fold increase in data volume. We anticipate that iEKPD 2.0 represents a more useful resource for further study of phosphorylation regulators.
Highlights
In eukaryotes, protein phosphorylation is one of the most studied post-translational modifications (PTMs); mainly occurs on specific serine, threonine or tyrosine residues of protein substrates; and participates in the regulation of almost all aspects of cellular activities, including cell proliferation, metabolism and cell death [1,2,3,4]
Protein phosphorylation is a reversibly dynamic process that is regulated by protein kinases (PKs) that provide the modification as ‘writers’ and protein phosphatases (PPs) that remove substrate modifications as ‘erasers’ [2,4,5,6]
As a gene-centered database, iEKPD 2.0 provided the classification and domain profile information for each phospho-regulator as well as a variety of basic annotations obtained from Ensembl [31] and UniProt [35] databases, such as protein/gene names/aliases, functional descriptions, Ensembl/UniProt/GeneBank/RefSeq accession numbers, protein/nucleotide sequences, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) terms, and domain/motifs
Summary
Protein phosphorylation is one of the most studied post-translational modifications (PTMs); mainly occurs on specific serine, threonine or tyrosine residues of protein substrates; and participates in the regulation of almost all aspects of cellular activities, including cell proliferation, metabolism and cell death [1,2,3,4]. We first collected 1860 PKs, 439 PPs and 400 PPBD-containing proteins from the literature and hierarchically classified them into 26 groups and 208 families (Figure 1). In addition to gene/protein names, accession numbers, classification information, functional descriptions, protein/nucleotide sequences and other types of basic annotations, we further integrated knowledge from 100 publicly available databases that covered 13 aspects.
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