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Bioinformatics Vol. 18 no. 5 2002
Pages 705-714
© 2002 Oxford University Press

Extraction of knowledge on protein--protein interaction by association rule discovery

T. Oyama 1,*, K. Kitano 1, K. Satou 2 and T. Ito 3

1 INTEC Web and Genome Informatics Corporation, 3-23, Shimoshin-machi, Toyama 930-0804, Japan
2 School of Knowledge Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan
3 Cancer Research Institute, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-0934, Japan

Received on June 10, 2001 ; revised on October 26, 2001 ; accepted on December 3, 2001

Motivation: Protein--protein interactions are systematically examined using the yeast two-hybrid method. Consequently, a lot of protein--protein interaction data are currently being accumulated. Nevertheless, general information or knowledge on protein--protein interactions is poorly extracted from these data. Thus we have been trying to extract the knowledge from the protein--protein interaction data using data mining.

Results: A data mining method is proposed to discover association rules related to protein--protein interactions. To evaluate the detected rules by the method, a new scoring measure of the rules is introduced. The method allowed us to detect popular interaction rules such as ‘An SH3 domain binds to a proline-rich region.’ These results indicate that the method may detect novel knowledge on protein--protein interactions.

Contact: oyama{at}isl.intec.co.jp

* To whom correspondence should be addressed.


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