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. 2016 Mar 24;6:23534.
doi: 10.1038/srep23534.

dbPAF: An Integrative Database of Protein Phosphorylation in Animals and Fungi

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Free PMC article

dbPAF: An Integrative Database of Protein Phosphorylation in Animals and Fungi

Shahid Ullah et al. Sci Rep. .
Free PMC article

Abstract

Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.

Figures

Figure 1
Figure 1. The procedure for the construction of dbPAF database.
Also, we also integrated know phosphorylation sites from several public databases, including Phospho.ELM, dbPTM, PHOSIDA, PhosphositePlus, PhosphoPep, PhosphoGRID, SysPTM, HPRD and UniProt.
Figure 2
Figure 2. The data statistics of dbPAF.
(a) The distribution of pS, pT and pT residues. (b) The distribution of phosphorylated proteins and sites in each species.
Figure 3
Figure 3. The “ Browse by species” option.
(a) Phosphorylated proteins can be browsed in a species-specific manner by clicking on the corresponding diagram. (b) The phosphorylated substrates will be listed in a tabular format. (c) The detailed annotations of human AGPS together with known phospho-sites.
Figure 4
Figure 4. The search options.
(a) “Substrate Search” with one or multiple keywords. (b) The “Advanced search” permitted users to input up to three terms for query. (c) The “Batch Search” for retrieveing multiple protein entries with a list of terms. (d) The database can be searched with a protein sequence in FASTA format to find identical or homolgous phosphoproteins.
Figure 5
Figure 5. Motif-based analysis of sequence preferences around phosphorylation sites in H. sapiens, M. musculus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae.
In each species, the most significant motif was visualized for each type of phosphorylated residue. In the default threshold, we did not detect any pY motifs for S. pombe, due to the data limitation. However, when we slightly relaxed the stringency, a significant pY motif was detected, with a p-value <0.00001.
Figure 6
Figure 6
The distrubtions of PKs that were predicted to modify phospho-sites in H. sapiens, M. musculus and R. norvegicus, (a) in the kinase group level, and (b) in the kinase family level.
Figure 7
Figure 7. The evolutionary analysis of phosphorylation conservation.
(a) As previously described, RCSp was calculated as RCR*MBL. (b) We further calculated rRCS values for phosphorylation sites, and the average rRCS values of pS, pT, pY and all sites were shown for each species.

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