| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH |
|
|
|
|||||||
|
|||||||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Submitted on December 26, 2001
DOE-MBI LSBMM, UCLA, Los Angeles, CA 90095-1507
Corresponding Author: david{at}mbi.ucla.edu
High-throughput methods for detecting protein interactions require assessment of their accuracy. We present two forms of computational assessment. The first method is the Expression Profile Reliability Index (EPR Index). The EPR index estimates the biologically relevant fraction of protein interactions detected in a high-throughput screen. It does so by comparing the RNA expression profiles for the proteins whose interactions are found in the screen with expression profiles for known interacting and non-interacting pairs of proteins. The second form of assessment is the Paralogous Verification Method (PVM). This method judges an interaction likely if the putatively interacting pair has paralogs that also interact. In contrast to the EPR index which evaluates datasets of interactions, PVM scores individual interactions. On a test set, PVM correctly identifies 40% of true interactions with a false positive rate of ~1%. EPR and PVM were applied to the Database of Interacting Proteins (DIP), a large and diverse collection of protein-protein interactions that contains over 8000 S. cerevisiae pairwise protein interactions. Using these two methods, we estimate that ~50% of them are reliable and with the aid of PVM we confidently identify 3003 of them. Web servers for both the PVM and EPR methods are available on the DIP website (http://dip.doe-mbi.ucla.edu/Services.cgi).
Revised on March 20, 2002
Accepted on April 4, 2002
Protein interactions: Two methods for assessment of the reliability of high-throughput observations
CiteULike 
Complore 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati What's this?
This article has been cited by other articles:
|
|
 |
|
  T.-t. Soong, K. O. Wrzeszczynski, and B. Rost Physical protein-protein interactions predicted from microarrays Bioinformatics, November 15, 2008; 24(22): 2608 - 2614. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Park, B.-C. Kim, S.-W. Cho, S.-J. Park, J.-S. Choi, S. I. Kim, J. Bhak, and S. Lee MassNet: a functional annotation service for protein mass spectrometry data Nucleic Acids Res., July 1, 2008; 36(suppl_2): W491 - W495. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Li, W. Liu, Z. Liu, J. Wang, Q. Liu, Y. Zhu, and F. He PRINCESS, a Protein Interaction Confidence Evaluation System with Multiple Data Sources Mol. Cell. Proteomics, June 1, 2008; 7(6): 1043 - 1052. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Guo, L. Yu, Z. Wen, and M. Li Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences Nucleic Acids Res., May 1, 2008; 36(9): 3025 - 3030. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 M. Koegl and P. Uetz Improving yeast two-hybrid screening systems Brief Funct Genomic Proteomic, January 24, 2008; (2008) elm035v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
P.-Y. Chen, C. M. Deane, and G. Reinert A statistical approach using network structure in the prediction of protein characteristics Bioinformatics, September 1, 2007; 23(17): 2314 - 2321. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Dawelbait, C. Winter, Y. Zhang, C. Pilarsky, R. Grutzmann, J.-C. Heinrich, and M. Schroeder Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data Bioinformatics, July 1, 2007; 23(13): i115 - i124. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Luo, Y. Yang, C.-F. Chen, R. Chang, J. Zhou, and R. H. Scheuermann Modular organization of protein interaction networks Bioinformatics, January 15, 2007; 23(2): 207 - 214. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Ma, H. Lee, L. Wang, and F. Sun CGI: a new approach for prioritizing genes by combining gene expression and protein-protein interaction data Bioinformatics, January 15, 2007; 23(2): 215 - 221. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
Y. Y. Shi, G. A. Miller, H. Qian, and K. Bomsztyk Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences PNAS, August 1, 2006; 103(31): 11527 - 11532. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Prieto and J. De Las Rivas APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W298 - W302. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Guo, R. Liu, C. D. Shriver, H. Hu, and M. N. Liebman Assessing semantic similarity measures for the characterization of human regulatory pathways Bioinformatics, April 15, 2006; 22(8): 967 - 973. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Makino and T. Gojobori The Evolutionary Rate of a Protein Is Influenced by Features of the Interacting Partners Mol. Biol. Evol., April 1, 2006; 23(4): 784 - 789. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. J. Deeds, O. Ashenberg, and E. I. Shakhnovich From The Cover: A simple physical model for scaling in protein-protein interaction networks PNAS, January 10, 2006; 103(2): 311 - 316. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Hwang, A. G. Rust, S. Ramsey, J. J. Smith, D. M. Leslie, A. D. Weston, P. de Atauri, J. D. Aitchison, L. Hood, A. F. Siegel, et al. A data integration methodology for systems biology PNAS, November 29, 2005; 102(48): 17296 - 17301. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Hwang, J. J. Smith, D. M. Leslie, A. D. Weston, A. G. Rust, S. Ramsey, P. de Atauri, A. F. Siegel, H. Bolouri, J. D. Aitchison, et al. A data integration methodology for systems biology: Experimental verification PNAS, November 29, 2005; 102(48): 17302 - 17307. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. E. Cusick, N. Klitgord, M. Vidal, and D. E. Hill Interactome: gateway into systems biology Hum. Mol. Genet., October 15, 2005; 14(suppl_2): R171 - R181. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. Miller, R. S. Lo, A. Ben-Hur, C. Desmarais, I. Stagljar, W. S. Noble, and S. Fields Large-scale identification of yeast integral membrane protein interactions PNAS, August 23, 2005; 102(34): 12123 - 12128. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Espadaler, R. Aragues, N. Eswar, M. A. Marti-Renom, E. Querol, F. X. Aviles, A. Sali, and B. Oliva Detecting remotely related proteins by their interactions and sequence similarity PNAS, May 17, 2005; 102(20): 7151 - 7156. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. R. Brown and I. Jurisica Online Predicted Human Interaction Database Bioinformatics, May 1, 2005; 21(9): 2076 - 2082. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Okada, S. Kanaya, and K. Asai Accurate extraction of functional associations between proteins based on common interaction partners and common domains Bioinformatics, May 1, 2005; 21(9): 2043 - 2048. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Albers, H. Kranz, I. Kober, C. Kaiser, M. Klink, J. Suckow, R. Kern, and M. Koegl Automated Yeast Two-hybrid Screening for Nuclear Receptor-interacting Proteins Mol. Cell. Proteomics, February 1, 2005; 4(2): 205 - 213. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. R. Said, T. J. Begley, A. V. Oppenheim, D. A. Lauffenburger, and L. D. Samson Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae PNAS, December 28, 2004; 101(52): 18006 - 18011. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 A. Gafni Proteomics in Aging-Related Research Sci. Aging Knowl. Environ., November 10, 2004; 2004(45): pe41 - pe41. [Abstract] [Full Text]
|
|
|
|
|
|
L. Terradot, N. Durnell, M. Li, M. Li, J. Ory, A. Labigne, P. Legrain, F. Colland, and G. Waksman Biochemical Characterization of Protein Complexes from the Helicobacter pylori Protein Interaction Map: Strategies for Complex Formation and Evidence for Novel Interactions Within Type IV Secretion Systems Mol. Cell. Proteomics, August 1, 2004; 3(8): 809 - 819. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Asthana, O. D. King, F. D. Gibbons, and F. P. Roth Predicting Protein Complex Membership Using Probabilistic Network Reliability Genome Res., June 1, 2004; 14(6): 1170 - 1175. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A.-C. Tien, M.-H. Lin, L.-J. Su, Y.-R. Hong, T.-S. Cheng, Y.-C. G. Lee, W.-J. Lin, I. H. Still, and C.-Y. F. Huang Identification of the Substrates and Interaction Proteins of Aurora Kinases from a Protein-Protein Interaction Model Mol. Cell. Proteomics, January 1, 2004; 3(1): 93 - 104. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
J. Zhong, H. Zhang, C. A. Stanyon, G. Tromp, and R. L. Finley Jr. A Strategy for Constructing Large Protein Interaction Maps Using the Yeast Two-Hybrid System:Regulated Expression Arrays and Two-Phase Mating Genome Res., December 1, 2003; 13(12): 2691 - 2699. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Qin, H. H. S. Lu, W. B. Wu, and W.-H. Li Evolution of the yeast protein interaction network PNAS, October 28, 2003; 100(22): 12820 - 12824. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Jansen, H. Yu, D. Greenbaum, Y. Kluger, N. J. Krogan, S. Chung, A. Emili, M. Snyder, J. F. Greenblatt, and M. Gerstein A Bayesian Networks Approach for Predicting Protein-Protein Interactions from Genomic Data Science, October 17, 2003; 302(5644): 449 - 453. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Wilhelm, H.-P. Nasheuer, and S. Huang Physical and Functional Modularity of the Protein Network in Yeast Mol. Cell. Proteomics, May 1, 2003; 2(5): 292 - 298. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. S. Goldberg and F. P. Roth Assessing experimentally derived interactions in a small world PNAS, April 15, 2003; 100(8): 4372 - 4376. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Ito, K. Ota, H. Kubota, Y. Yamaguchi, T. Chiba, K. Sakuraba, and M. Yoshida Roles for the Two-hybrid System in Exploration of the Yeast Protein Interactome Mol. Cell. Proteomics, August 1, 2002; 1(8): 561 - 566. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH |
| All ASBMB Journals | Journal of Biological Chemistry |
| Journal of Lipid Research | ASBMB Today |
