Observation of the Correlations between Pair Wise Interaction and Functional Organization of the Proteins, in the Protein Interaction Network of Saccaromyces Cerevisiae
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.
[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
[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
@article{"International Journal of Chemical, Materials and Biomolecular Sciences:53923", author = "N. Tuncbag and T. Haliloglu and O. Keskin", title = "Observation of the Correlations between Pair Wise Interaction and Functional Organization of the Proteins, in the Protein Interaction Network of Saccaromyces Cerevisiae", 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.", volume = "2", number = "8", pages = "191-6", }