Skip Navigation


Bioinformatics Advance Access originally published online on May 24, 2005
Bioinformatics 2005 21(15):3234-3240; doi:10.1093/bioinformatics/bti512
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/15/3234    most recent
bti512v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (11)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Park, D.
Right arrow Articles by Bhak, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Park, D.
Right arrow Articles by Bhak, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published by Oxford University Press 2005

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

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

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

*To whom correspondence should be addressed.

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 to the evolution of interactomes and seemed tohave played a key role in species diversification.

Contact: jong{at}kribb.re.kr

Supplementary information: http://interactomics.org

Received on February 28, 2005; revised on April 22, 2005; accepted on May 19, 2005

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
J. Cui, P. Li, G. Li, F. Xu, C. Zhao, Y. Li, Z. Yang, G. Wang, Q. Yu, Y. Li, et al.
AtPID: Arabidopsis thaliana protein interactome database an integrative platform for plant systems biology
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D999 - D1008.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Q. Xu, A. Canutescu, Z. Obradovic, and R. L. Dunbrack Jr
ProtBuD: a database of biological unit structures of protein families and superfamilies
Bioinformatics, December 1, 2006; 22(23): 2876 - 2882.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.