dbPAF Edit

Citations: 8

z-index: 4

Basic information
Short name dbPAF
Full name Database of phospho-sites in Animals and Fungi
Description The dbPAF (database of Phospho-sites in Animals and Fungi) is an online data resource specifically designed for protein phosphorylation in seven eukaryotic species, including H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature, 294,370 non-redundant phosphorylation sites of 40,432 proteins were collected. Phosphorylation sites from a number of public databases such as Phospho.ELM, dbPTM, PhosphoPep were integrated.
URL http://dbpaf.biocuckoo.org
Year founded
Last update & version
Availability Free to academic users only
Contact information
University/Institution hosted Huazhong University of Science and Technology
Address Department of Bioinformatics & Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
City Wuhan
Province/State
Country/Region China
Contact name Yu Xue
Contact email xueyu@hust.edu.cn
Data information
Object(s)
  • Animal
  • Fungi
Data type(s)
  • Protein
Data Category/Categories
  • Modification
Major organism(s)
  • Homo sapiens
  • Mus musculus
  • Drosophila melanogaster
  • Caenorhabditis elegans
  • Saccharomyces cerevisiae
Keyword(s)
  • protein phosphorylation
  • dbPAF
  • post-translational modifications
Publications
  • dbPAF: an integrative database of protein phosphorylation in animals and fungi.[PMID: 27010073]
    Shahid Ullah, Shaofeng Lin, Yang Xu, Wankun Deng, Lili Ma, Ying Zhang, Zexian Liu, Yu Xue,

    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.

    Sci Rep 2016:6()

    8 Citations (from Europe PMC, 2018-10-12)

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Record metadata

  • Created on: 2018-01-28
    • Nazir Farah [2018-04-07]

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