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Bioinformatics Advance Access published online on June 24, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth366
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received November 10, 2003
Revised May 17, 2004
Accepted June 4, 2004

Applications note

POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome

Tao-Wei Huang 1, An-Chi Tien 2, Wen-Shien Huang 3, Yuan-Chii G. Lee 4, Chin-Lin Peng 3, Huei-Hun Tseng 1, Cheng-Yan Kao 3, Chi-Ying F. Huang 5*

1 Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan, Republic of China; Department of Computer Science and Information Engineering, National Taiwan University, Taiwan 106, Republic of China
2 Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan, Republic of China
3 Department of Computer Science and Information Engineering, National Taiwan University, Taiwan 106, Republic of China
4 Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan, Republic of China; Graduate Institute of Medical Informatics, Taipei Medical University, Taipei 110, Taiwan, Republic of China
5 Division of Molecular and Genomic Medicine, National Health Research Institutes, Taipei 115, Taiwan, Republic of China; Department of Computer Science and Information Engineering, National Taiwan University, Taiwan 106, Republic of China; Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan, Republic of China

* To whom correspondence should be addressed. E-mail: chiying{at}nhri.org.tw.


  Abstract

Summary: One possible path towards understanding the biological function of a target protein is through the discovery of how it interfaces within protein-protein interaction networks. The goal of this study was to create a virtual protein-protein interaction model using the concepts of orthologous conservation (or interologs) to elucidate the interacting networks of a particular target protein. POINT (the prediction of interactome database) is a functional database for the prediction of the human protein-protein interactome based on available orthologous interactome datasets. POINT integrates several publicly accessible databases, with emphasis placed on the extraction of a large quantity of mouse, fruit fly, worm and yeast protein-protein interactions datasets from the Database of Interacting Proteins (DIP), followed by conversion of them into a predicted human interactome. In addition, protein-protein interactions require both temporal synchronicity and precise spatial proximity. POINT therefore also incorporates correlated mRNA expression clusters obtained from cell cycle microarray databases and subcellular localization from Gene Ontology to further pinpoint the likelihood of biological relevance of each predicted interacting sets of protein partners.

Availability: The POINT can be freely accessed at http://insilico.csie.ntu.edu.tw:9999/point/.


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