The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast

Nucleic Acids Research
Hongchao LuRunsheng Chen

Abstract

The refinement and high-throughput of protein interaction detection methods offer us a protein-protein interaction network in yeast. The challenge coming along with the network is to find better ways to make it accessible for biological investigation. Visualization would be helpful for extraction of meaningful biological information from the network. However, traditional ways of visualizing the network are unsuitable because of the large number of proteins. Here, we provide a simple but information-rich approach for visualization which integrates topological and biological information. In our method, the topological information such as quasi-cliques or spoke-like modules of the network is extracted into a clustering tree, where biological information spanning from protein functional annotation to expression profile correlations can be annotated onto the representation of it. We have developed a software named PINC based on our approach. Compared with previous clustering methods, our clustering method ADJW performs well both in retaining a meaningful image of the protein interaction network as well as in enriching the image with biological information, therefore is more suitable in visualization of the network.

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Citations

Dec 19, 2008·Journal of the Royal Society, Interface·Joana P GonçalvesAndré X C N Valente
Nov 8, 2006·BMC Bioinformatics·Sylvain Brohée, Jacques van Helden
Sep 18, 2010·BMC Systems Biology·Mahnaz HabibiLimsoon Wong
Apr 26, 2008·PLoS Computational Biology·Liping Wei, Jun Yu
Jul 21, 2010·PloS One·Rodrigo Aldecoa, Ignacio Marín
May 24, 2006·Nucleic Acids Research·André X C N Valente, Michael E Cusick
May 7, 2014·BioMed Research International·Ru Shen, Chittibabu Guda
Nov 14, 2006·Computational Biology and Chemistry·Shihua ZhangXiang-Sun Zhang
Aug 25, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jianxin WangYi Pan
Dec 23, 2014·IEEE Transactions on Cybernetics·Liang YangDan Meng
May 13, 2006·Biochemical and Biophysical Research Communications·Hongchao LuRunsheng Chen
Oct 8, 2008·Cellular & Molecular Biology Letters·Dariusz Plewczyński, Krzysztof Ginalski
Mar 15, 2005·Yeast
May 5, 2005·The Journal of Biological Chemistry·Marcus KlotzscheWolfgang Hillen
Apr 21, 2020·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Edwin K SilvermanJan Baumbach

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