Functional evaluation of domain–domain interactions and human protein interaction networks
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany
*To whom correspondence should be addressed.
 |
Abstract |
|---|
Motivation: Large amounts of protein and domain interaction data are being produced by experimental high-throughput techniques and computational approaches. To gain insight into the value of the provided data, we used our new similarity measure based on the Gene Ontology (GO) to evaluate the molecular functions and biological processes of interacting proteins or domains. The applied measure particularly addresses the frequent annotation of proteins or domains with multiple GO terms.
Results: Using our similarity measure, we compare predicted domain–domain and human protein–protein interactions with experimentally derived interactions. The results show that our similarity measure is of significant benefit in quality assessment and confidence ranking of domain and protein networks. We also derive useful confidence score thresholds for dividing domain interaction predictions into subsets of low and high confidence.
Contact: mario.albrecht{at}mpi-inf.mpg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Associate Editor: Dmitrij Frishman
Received on October 31, 2006; revised on December 23, 2006; accepted on January 14, 2007
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. Schlicker and M. Albrecht FunSimMat update: new features for exploring functional similarity Nucleic Acids Res., November 18, 2009; (2009) gkp979v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Blankenburg, R. D. Finn, A. Prlic, A. M. Jenkinson, F. Ramirez, D. Emig, S.-E. Schelhorn, J. Buch, T. Lengauer, and M. Albrecht DASMI: exchanging, annotating and assessing molecular interaction data Bioinformatics, May 15, 2009; 25(10): 1321 - 1328. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Emig, M. S. Cline, T. Lengauer, and M. Albrecht Integrating expression data with domain interaction networks Bioinformatics, November 1, 2008; 24(21): 2546 - 2548. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S.-E. Schelhorn, T. Lengauer, and M. Albrecht An integrative approach for predicting interactions of protein regions Bioinformatics, August 15, 2008; 24(16): i35 - i41. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Pandey, M. Koyuturk, S. Subramaniam, and A. Grama Functional coherence in domain interaction networks Bioinformatics, August 15, 2008; 24(16): i28 - i34. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Schlicker and M. Albrecht FunSimMat: a comprehensive functional similarity database Nucleic Acids Res., January 11, 2008; 36(suppl_1): D434 - D439. [Abstract] [Full Text] [PDF]
|
|