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KANPHOS Platform: A new platform in INCF J-Node for neural phosphoproteomics

Junichiro Yoshimoto1, 2*, Takayuki Kannon3, 4, Mutsuki Amano5, Tomoki Nishioka5, Shiro Usui4 and Kozo Kaibuchi5
  • 1 Nara Institute of Science and Technology, Graduate School of Information Science, Japan
  • 2 Okinawa Institute of Science and Technology Graduate University, Japan
  • 3 Kanazawa University, Graduate School of Medical Sciences, Japan
  • 4 RIKEN Brain Science Institute, Neuroinformatics Japan Center, Japan
  • 5 Nagoya University Graduate School of Medicine, Department of Cell Pharmacology, Japan

Protein phosphorylation is involved in a variety of intracellular signaling pathways and physiological functions in the nervous system. While recent advances in mass spectrometry based proteomics allowed us to identify approximately 200,000 phosphorylation sites [1], it is not fully understood which sites are phosphorylated by a specific kinase and which extracellular stimuli regulate the protein phosphorylation via intracellular signaling cascades. To uncover the basic issue, we developed a new methodology for comprehensive screening of the target phosphorylation sites of a given kinase (or extracellular signal) [2,3]. In this demonstration, we present an on-line database system that provides the phosphorylation signals identified by our developed methodology as well as those previously reported in the literature. The database system and its web portal were built based on the Next Generation XooNIps [4], and named “KANPHOS (Kinase-Associated PHOspho-Signaling).” All data are controlled for quality via review and curation by our professional staffs. In the portal site, we can search for the data of interest in three ways: 1) Search for substrates phosphorylated by a specific kinase; 2) Search for kinases phosphorylating a specific protein; and 3) Search for kinases and their target substrates by a specific signaling pathway. Each substrate is associated with basic information provided by the UniProt Knowledgebase (UniProtKB) such as protein and gene name synonyms and description about physiological functions. Also, to allow the users for cross-searching with minimal efforts, each entry has hyperlinks to external databases (e.g. KEGG PATHWAY Database, GeneCards, and Allen Brain Atlas). For the sustainability of the database, we launched the KANPHOS Platform in INCF Japan Node in April, 2016. We will discuss future challenges of this platform and collaboration plans with other platforms in the demonstration.

Acknowledgements

This study was supported by “Bioinformatics for Brain Sciences” carried out under the Strategic Research Program for Brain Sciences by the MEXT, Japan, and Neuroinformatics Japan Center, RIKEN Brain Science Institute.

References

[1] Hornbeck, P. V, et al. (2015). PhosphoSitePlus, 2014: mutations, PTMs and recalibrations. Nucleic Acids Res. 43, D512–D520.
[2] Amano, M., et al. (2015). Kinase-interacting substrate screening is a novel method to identify kinase substrates. J. Cell Biol. 209, 895–912.
[3] Nishioka, T., et al. (2015). Developing novel methods to search for substrates of protein kinases such as Rho-kinase. Biochim. Biophys. Acta - Proteins Proteomics 1854, 1663–1666.
[4] Kannon, T., et al. (2014). Next Generation XooNIps. In Advances in Neuroinformatics 2014, RI-5, http://dx.doi.org/10.14931/aini2014.ri.5.

Keywords: phosphoproteomics, Signaling Pathways, neuroinformatics platform, XooNIps, Kinase-interacting substrate screening

Conference: Neuroinformatics 2016, Reading, United Kingdom, 3 Sep - 4 Sep, 2016.

Presentation Type: Demo

Topic: General neuroinformatics

Citation: Yoshimoto J, Kannon T, Amano M, Nishioka T, Usui S and Kaibuchi K (2016). KANPHOS Platform: A new platform in INCF J-Node for neural phosphoproteomics. Front. Neuroinform. Conference Abstract: Neuroinformatics 2016. doi: 10.3389/conf.fninf.2016.20.00045

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Received: 30 Apr 2016; Published Online: 18 Jul 2016.

* Correspondence: Dr. Junichiro Yoshimoto, Nara Institute of Science and Technology, Graduate School of Information Science, Nara, 630-0192, Japan, junichiro.yoshimoto@fujita-hu.ac.jp