The Mammalian Protein–Protein Interaction Database and Its Viewing System That Is Linked to the Main FANTOM2 Viewer

  1. Harukazu Suzuki1,3,6,
  2. Rintaro Saito1,5,
  3. Mutsumi Kanamori1,
  4. Chikatoshi Kai1,
  5. Christian Schönbach4,
  6. Takeshi Nagashima4,
  7. Junko Hosaka4, and
  8. Yoshihide Hayashizaki1,2,3
  1. 1Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
  2. 2Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan
  3. 3JST-CREST, Saitama 351-0198, Japan
  4. 4Biomedical Knowledge Discovery Team, Bioinformatics Group, RIKEN Genomic Sciences Center (GSC), Yokohama 230-0045, Japan

Abstract

Here, we describe the development of a mammalian protein–protein interaction (PPI) database and of a PPI Viewer application to display protein interaction networks (http://fantom21.gsc.riken.go.jp/PPI/). In the database, we stored the mammalian PPIs identified through our PPI assays (internal PPIs), as well as those we extracted and processed (external PPIs) from publicly available data sources, the DIP and BIND databases and MEDLINE abstracts by using FACTS, a new functional inference and curation system. We integrated the internal and external PPIs into the PPI database, which is linked to the main FANTOM2 viewer. In addition, we incorporated into the PPI Viewer information regarding the luciferase reporter activity of internal PPIs and the data confidence of external PPIs; these data enable visualization and evaluation of the reliability of each interaction. Using the described system, we successfully identified several interactions of biological significance. Therefore, the PPI Viewer is a useful tool for exploring FANTOM2 clone-related protein interactions and their potential effects on signaling and cellular communication.

Footnotes

  • [The protein–protein interaction data that have been derived from our experiments and are newly described in this paper have been submitted to the BIND database.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.956303.

  • ↵6 Corresponding author. E-MAIL rgscerg{at}gsc.riken.go.jp; FAX (81) 45-503-9216.

  • ↵5 Present address: Institute for Advanced Biosciences, Keio University, Yamagata 997-0035, Japan

    • Accepted March 3, 2003.
    • Received November 5, 2002.
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  1. doi: 10.1101/gr.956303 Genome Res. 13: 1534-1541 Cold Spring Harbor Laboratory Press

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