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Bioinformatics Advance Access published online on May 24, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti512
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 28, 2005
Revised April 22, 2005
Accepted May 19, 2005

Article

Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)

Daeui Park 1, Semin Lee 2, Dan Bolser 3, Michael Schroeder 4, Michael Lappe 5, Donghoon Oh 1, and Jong Bhak 6*

1 Object Interaction Technologies Inc., CMS Building 705, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, KOREA
2 Department of BioSystems, KAIST, 373-1, Yuseong-gu, Daejeon 305-701, KOREA
3 Medical Research Council, Dunn Human Nutrition Unit, Cambridge, CB2 2QH, UK
4 Biotec and Department of Computing, TU Dresden, 108 01307 Dresden, GERMANY
5 Max-Planck-Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, GERMANY
6 Department of BioSystems, KAIST, 373-1, Yuseong-gu, Daejeon 305-701, KOREA; NGIC, KRIBB, Daejeon 305-333, Korea

* To whom correspondence should be addressed.
Jong Bhak, E-mail: jong{at}kribb.re.kr


  Abstract

Motivation: Many genomes have been completely sequenced. However, detecting and analyzing their protein-protein interactions by experimental methods such as co-immunoprecipitation, tandem affinity purification, and Y2H is not as fast as genome sequencing. Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein-protein interaction rules within and among complete genomes.

Results: We confirmed that all the predicted protein family interactomes (the full set of protein family interactions within a proteome) of 146 species are scale-free networks, and they share a small core network comprising 36 protein families related to indispensable cellular functions. We found two fundamental differences among prokaryotic and eukaryotic interactomes: 1) eukarya had significantly more hub families than archaea and bacteria, and 2) certain special hub families determined the topology of the eukaryotic interactomes. Our comparative analysis suggests that a very small number of expansive protein families led the evolution of interactomes and seemed to have played a key role in species diversification.

Supplementary Information: Supplementary data: Figure 1, Table 4.


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