Skip Navigation



Bioinformatics Advance Access published online on June 1, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm294
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/16/2121    most recent
btm294v2
btm294v1
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Guo, Z.
Right arrow Articles by Wang, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Guo, Z.
Right arrow Articles by Wang, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network

Zheng Guo 1,2,*, Yongjin Li 1, Xue Gong 1, Chen Yao 1, Wencai Ma 1, Dong Wang 1, Yanhui Li 1, Jing Zhu 1, Min Zhang 1, Da Yang 1 and Jing Wang 1

1 Department of Bioinformatics, Bio-pharmaceutical Key Laboratory of Heilongjiang Province-Incubator of State Key Laboratory, Harbin Medical University, Harbin 150086, China
2 Bioinformatics Centre and School of Life Science, University of Electronic Science and Technology of China, Chengdu, 610054, China

*To whom correspondence should be addressed. Prof. Zheng Guo, E-mail: guoz{at}ems.hrbmu.edu.cn


  Abstract

Motivation: Current high-throughput protein-protein interaction (PPI) data do not provide information about the condition(s) under which the interactions occur. Thus, the identification of condition-responsive PPI sub-networks is of great importance for investigating how a living cell adapts to changing environments.

Results: In this paper, we propose a novel edge-based scoring and searching approach to extract a PPI sub-network responsive to conditions related to some investigated gene expression profiles. Using this approach, what we constructed is a sub-network connected by the selected edges (interactions), instead of only a set of vertices (proteins) as in previous works. Furthermore, we suggest a systematic approach to evaluate the biological relevance of the identified responsive sub-network by its ability of capturing condition-relevant functional modules. We apply the proposed method to analyze a human prostate cancer dataset and a yeast cell cycle dataset. The results demonstrate that the edge-based method is able to efficiently capture relevant protein interaction behaviors under the investigated conditions.

Associate Editor: Prof. Alfonso Valencia

Received on January 14, 2007; revised on May 19, 2007; accepted on May 25, 2007

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
 BioinformaticsHome page
I. Ulitsky and R. Shamir
Identifying functional modules using expression profiles and confidence-scored protein interactions
Bioinformatics, May 1, 2009; 25(9): 1158 - 1164.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Z. Sun, J. Luo, Y. Zhou, J. Luo, K. Liu, and W. Li
Exploring phenotype-associated modules in an oral cavity tumor using an integrated framework
Bioinformatics, March 15, 2009; 25(6): 795 - 800.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. Zhang, C. Yao, Z. Guo, J. Zou, L. Zhang, H. Xiao, D. Wang, D. Yang, X. Gong, J. Zhu, et al.
Apparently low reproducibility of true differential expression discoveries in microarray studies
Bioinformatics, September 15, 2008; 24(18): 2057 - 2063.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. T. Dittrich, G. W. Klau, A. Rosenwald, T. Dandekar, and T. Muller
Identifying functional modules in protein-protein interaction networks: an integrated exact approach
Bioinformatics, July 1, 2008; 24(13): i223 - i231.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
D. Yang, Y. Li, H. Xiao, Q. Liu, M. Zhang, J. Zhu, W. Ma, C. Yao, J. Wang, D. Wang, et al.
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories
Bioinformatics, January 15, 2008; 24(2): 265 - 271.
[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.