Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental Research Data
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
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 Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Deng, M.
Right arrow Articles by Chen, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Deng, M.
Right arrow Articles by Chen, T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 12, Issue 10, 1540-1548, October 2002

LETTER
Inferring Domain-Domain Interactions From Protein-Protein Interactions

Minghua Deng, Shipra Mehta, Fengzhu Sun,1,2 and Ting Chen1,3

Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA

The interaction between proteins is one of the most important features of protein functions. Behind protein-protein interactions there are protein domains interacting physically with one another to perform the necessary functions. Therefore, understanding protein interactions at the domain level gives a global view of the protein interaction network, and possibly of protein functions. Two research groups used yeast two-hybrid assays to generate 5719 interactions between proteins of the yeast Saccharomyces cerevisiae. This allows us to study the large-scale conserved patterns of interactions between protein domains. Using evolutionarily conserved domains defined in a protein-domain database called PFAM (http://PFAM.wustl.edu), we apply a Maximum Likelihood Estimation method to infer interacting domains that are consistent with the observed protein-protein interactions. We estimate the probabilities of interactions between every pair of domains and measure the accuracies of our predictions at the protein level. Using the inferred domain-domain interactions, we predict interactions between proteins. Our predicted protein-protein interactions have a significant overlap with the protein-protein interactions (MIPS: http://mips.gfs.de) obtained by methods other than the two-hybrid assays. The mean correlation coefficient of the gene expression profiles for our predicted interaction pairs is significantly higher than that for random pairs. Our method has shown robustness in analyzing incomplete data sets and dealing with various experimental errors. We found several novel protein-protein interactions such as RPS0A interacting with APG17 and TAF40 interacting with SPT3, which are consistent with the functions of the proteins.

[Supplementary material is available online at http://www.genome.org and http://www-hto.usc.edu/~msms/ProteinInteraction.]

1 Corresponding authors.

2 E-MAIL fsun{at}hto.usc.edu.

3 E-MAIL tingchen{at}hto.usc.edu; FAX (213) 740-2424.

12:1540-1548 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
J. Guo, X. Wu, D.-Y. Zhang, and K. Lin
Genome-wide inference of protein interaction sites: lessons from the yeast high-quality negative protein-protein interaction dataset
Nucleic Acids Res., April 1, 2008; 36(6): 2002 - 2011.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. Saeed and C. Deane
An assessment of the uses of homologous interactions
Bioinformatics, March 1, 2008; 24(5): 689 - 695.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
B. Raghavachari, A. Tasneem, T. M. Przytycka, and R. Jothi
DOMINE: a database of protein domain interactions
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D656 - D661.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Pagel, M. Oesterheld, O. Tovstukhina, N. Strack, V. Stumpflen, and D. Frishman
DIMA 2.0 predicted and known domain interactions
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D651 - D655.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y.-C. Chen, Y.-S. Lo, W.-C. Hsu, and J.-M. Yang
3D-partner: a web server to infer interacting partners and binding models
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W561 - W567.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
B. Andreopoulos, A. An, X. Wang, M. Faloutsos, and M. Schroeder
Clustering by common friends finds locally significant proteins mediating modules
Bioinformatics, May 1, 2007; 23(9): 1124 - 1131.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Schlicker, C. Huthmacher, F. Ramirez, T. Lengauer, and M. Albrecht
Functional evaluation of domain domain interactions and human protein interaction networks
Bioinformatics, April 1, 2007; 23(7): 859 - 865.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. J. Cockell, B. Oliva, and R. M. Jackson
Structure-based evaluation of in silico predictions of protein protein interactions using Comparative Docking
Bioinformatics, March 1, 2007; 23(5): 573 - 581.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
E. Sprinzak, Y. Altuvia, and H. Margalit
Colloquium Papers: Characterization and prediction of protein-protein interactions within and between complexes
PNAS, October 3, 2006; 103(40): 14718 - 14723.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Chen, W. Hsu, M. L. Lee, and S.-K. Ng
Increasing confidence of protein interactomes using network topological metrics
Bioinformatics, August 15, 2006; 22(16): 1998 - 2004.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
E. Song, S. Gao, R. Tian, S. Ma, H. Huang, J. Guo, Y. Li, L. Zhang, and Y. Gao
A High Efficiency Strategy for Binding Property Characterization of Peptide-binding Domains
Mol. Cell. Proteomics, August 1, 2006; 5(8): 1368 - 1381.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Xing, T. Yu, Y. N. Wu, M. Roy, J. Kim, and C. Lee
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
Nucleic Acids Res., June 6, 2006; 34(10): 3150 - 3160.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
W. P. Lehrach, D. Husmeier, and C. K. I. Williams
A regularized discriminative model for the prediction of protein-peptide interactions
Bioinformatics, March 1, 2006; 22(5): 532 - 540.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X.-W. Chen and M. Liu
Prediction of protein-protein interactions using random decision forest framework
Bioinformatics, December 15, 2005; 21(24): 4394 - 4400.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Liu, N. Liu, and H. Zhao
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms
Bioinformatics, August 1, 2005; 21(15): 3279 - 3285.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. R. Brown and I. Jurisica
Online Predicted Human Interaction Database
Bioinformatics, May 1, 2005; 21(9): 2076 - 2082.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. S. Moon, J. Bhak, K. H. Lee, and D. Lee
Architecture of basic building blocks in protein and domain structural interaction networks
Bioinformatics, April 15, 2005; 21(8): 1479 - 1486.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. M. W. Nye, C. Berzuini, W. R. Gilks, M. M. Babu, and S. A. Teichmann
Statistical analysis of domains in interacting protein pairs
Bioinformatics, April 1, 2005; 21(7): 993 - 1001.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. D. Finn, M. Marshall, and A. Bateman
iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
Bioinformatics, February 1, 2005; 21(3): 410 - 412.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
H. Li and J. Li
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets
Bioinformatics, February 1, 2005; 21(3): 314 - 324.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D.-S. Han, H.-S. Kim, W.-H. Jang, S.-D. Lee, and J.-K. Suh
PreSPI: a domain combination based prediction system for protein-protein interaction
Nucleic Acids Res., December 1, 2004; 32(21): 6312 - 6320.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Salwinski, C. S. Miller, A. J. Smith, F. K. Pettit, J. U. Bowie, and D. Eisenberg
The Database of Interacting Proteins: 2004 update
Nucleic Acids Res., January 1, 2004; 32(90001): D449 - 451.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Lu, M. Hallett, S. Pollock, and D. Thomas
DePIE: Designing Primers for Protein Interaction Experiments
Nucleic Acids Res., July 1, 2003; 31(13): 3755 - 3757.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.