title: dbPAF: an integrative database of protein phosphorylation in animals and fungi.
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.
authors.affiliation: Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Shahid
authors.initials: S
authors.lastname: Ullah
authors.affiliation: Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Shaofeng
authors.initials: S
authors.lastname: Lin
authors.affiliation: Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Wankun
authors.initials: W
authors.lastname: Deng
authors.affiliation: Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Ma
authors.affiliation: Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Zexian
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Bioinformatics &Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.|Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Xue
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism*; D010766:Phosphorylation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D018511:Systems Integration
chemical_list: D005656:Fungal Proteins; D011506:Proteins