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Observation of the Correlations between Pair Wise Interaction and Functional Organization of the Proteins, in the Protein Interaction Network of Saccaromyces Cerevisiae

Authors: N. Tuncbag, T. Haliloglu, O. Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1059901

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References:


[1] S.-H. Yook, Z. N. Oltvai, A. L. Barabasi "Functional and topological characterization of protein interaction networks" in Proteomics, 2004, pp. 928-942.
[2] A.-L. Barabasi, Z. N. Oltvai "Network Biology: Understanding the Cell-s Functional Organization" in Genetics, 2004, pp. 101-111.
[3] L. Salwinski, C.S. Miller, A.J. Smith, F.K. Pettit, J.U. Bowie, D. Eisenberg "The Database of Interacting Proteins: 2004 update" in Nucleic Acids Research, 2004, pp.D449-51
[4] I. Xenarios, L. Salvinski, X. J. Duan, P. Higney, S.-M. Kim, D. Eisenberg "DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions" in Nucleic Acids Research, 2002, pp. 303-305.
[5] Gene Ontology Consortium, "Gene Ontology (GO) project in 2006 ", in Nucleic Acids Research, 2006, pp. D322-326.
[6] O. Keskin, "Comparison of Full-atomic and Coarse-grained Models to Examine The Molecular Fluctuations of c-AMP Dependent Protein Kinase", in Biomolecular Structure and Dynamics, 2002, pp. 1-13.
[7] L. N. Trefethen, D. Bau, Numerical Linear Algebra. Washington: Siam, 1997, ch.2.
[8] D. Raicu. (2004, February). Statistics with MATLAB. Available: http://facweb.cs.depaul.edu/Dstan/teaching/tutorials/Statistics%20with% 20Matlab.pdf
[9] R. Shamir, A. Maron-Katz, A. Tanay, Chaim Linhart, I. Steinfeld, R. Sharan, Y. Shiloh, R. Elkon " EXPANDER - an integrative program suite for microarray data analysis", in BMC Bioinformatics, 2005, 6:232