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Bioinformatics Vol. 19 Suppl. 1 2003
Pages i177-i179
© 2003 Oxford University Press

Complexity management in visualizing protein interaction networks

Byong-Hyon Ju and Kyungsook Han *

School of Computer Science & Engineering, Inha University, Inchon 402-751, Korea

Received on January 6, 2003 ; accepted on February 20, 2003

Motivation: Protein-protein interaction networks often consist of thousands of nodes or more. This severely limits the utility of many graph drawing tools because they become too slow for an interactive analysis of the networks and because they produce cluttered drawings with many edge crossings.

Results: A new layout algorithm with complexity management operations in visualizing a large-scale protein interaction network was developed and implemented in a program called InterViewer3. InterViewer3 simplifies a complex network by collapsing a group of nodes with the same interacting partners into a composite node and by replacing a clique with a star-shaped subgraph. The experimental results demonstrated that InterViewer3 is one order of magnitude faster than the other drawing programs and that its complexity management is successful.

Availability: http://wilab.inha.ac.kr/protein/

Contact: khan{at}inha.ac.kr

Keywords: protein-protein interaction network, visualization, abstraction

* To whom correspondence should be addressed.


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