The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 Viewer

Harukazu Suzuki, Rintaro Saito, Mutsumi Kanamori, Chikatoshi Kai, Christian Schönbach, Takeshi Nagashima, Junko Hosaka, Yoshihide Hayashizaki

Research output: Contribution to journalArticle

21 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1534-1541
Number of pages8
JournalGenome Research
Volume13
Issue number6 B
DOIs
Publication statusPublished - Jun 1 2003
Externally publishedYes

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Protein Databases
Proteins
Databases
Protein Interaction Maps
Information Storage and Retrieval
Luciferases
MEDLINE

ASJC Scopus subject areas

  • Genetics

Cite this

The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 Viewer. / Suzuki, Harukazu; Saito, Rintaro; Kanamori, Mutsumi; Kai, Chikatoshi; Schönbach, Christian; Nagashima, Takeshi; Hosaka, Junko; Hayashizaki, Yoshihide.

In: Genome Research, Vol. 13, No. 6 B, 01.06.2003, p. 1534-1541.

Research output: Contribution to journalArticle

Suzuki, H, Saito, R, Kanamori, M, Kai, C, Schönbach, C, Nagashima, T, Hosaka, J & Hayashizaki, Y 2003, 'The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 Viewer', Genome Research, vol. 13, no. 6 B, pp. 1534-1541. https://doi.org/10.1101/gr.956303
Suzuki, Harukazu ; Saito, Rintaro ; Kanamori, Mutsumi ; Kai, Chikatoshi ; Schönbach, Christian ; Nagashima, Takeshi ; Hosaka, Junko ; Hayashizaki, Yoshihide. / The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 Viewer. In: Genome Research. 2003 ; Vol. 13, No. 6 B. pp. 1534-1541.
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