Effective pre-processing strategies for functional clustering of a protein-protein interactions network

Proceedings - BIBE 2005: 5th IEEE Symposium on Bioinformatics and Bioengineering

Volumn 2005, Issue , 2005, Pages 129-136

  Ucar, Duygu ^a   Parthasarathy, Srinivasan ^a   Asur, Sitaram ^a   Chao, Wang ^a  

^a Ohio State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MULTILEVEL GRAPH PARTITIONING; PROTEIN PROTEIN INTERACTION (PPI); STATISTICAL METRICS;

COMPUTATIONAL METHODS; FUNCTION EVALUATION; GRAPHIC METHODS; MATHEMATICAL TRANSFORMATIONS; STATISTICAL METHODS; THEOREM PROVING;

PROTEINS;

EID: 33751192668     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2005.25     Document Type: Conference Paper

References (19)

1. http://www-users.cs.umn.edu//karypis//cluto//index.html.
2. http://www-users.cs.umn.edu/karypis/metis/metis/files/manual.pdf.
3. http://db.yeastgenome.org/cgi-bin/GO/goTermFinder.
4. http://www.fas.at.
5. M. Ashburner and et al. Gene ontology: tool for the unification of biology, the gene ontology consortium. Nat Genet., 25(1):25-29, May 2000.
6. C. Brun, C. Herrmann, and A. Guenoche. Clustering proteins from interaction networks for the prediction of cellular functions. BMC Bioinformatics, 5(95), July 2004.
7. C. Deane, L. Salwinski, I. Xenarios, and D. Eisenberg. Two methods for assessment of the reliability of high throughput observations. Molecular and Cellular Proteomics, 1(5):349-356, May 2002.
8. S. Fields and O. Song. A novel genetic system to detect protein-protein interactions. Nature, 340(6230):245-246, July 1989.
9. L. Freeman. Centrality in social networks: Conceptual clarification. Social Networks, 1:215-239, 1979.
10. L. Freeman. Centered graphs and the construction of ego networks. Mathematical Social Sciences, 3, 1982.
11. J. Hua, D. Koes, and Z. Kou. Finding motifs in protein-protein interaction networks. Project Final Report, CMU, 2003.
12. J. Nacher, T. Yamada, S. Goto, M. Kanehisa, and T. Akutsu. Two complementary representations of a scale-free network. Physica A, 349:349-363, 2005.
13. J. Pereira-Leal, A. Enright, and C. Ouzounis. Detection of functional modules from protein interaction networks. Proteins, 54(1):49-57, January 2004.
14. R. Saito and et al. Interaction generality, a measurement to assess the reliability of a protein protein interaction. Nucleic Acids Research, 30(5):1163-1168, March 2002.
15. S. Skiena. Line graph 4.1.5 in implementing discrete mathematics: Combinatorics and graph theory with mathematica. Reading, MA: Addison-Wesley, pp. 128 and 135-139, 1990.
16. A. Thomas, R. Cannings, N. Monk, and C. Cannings. On the structure of protein-protein interaction networks. Biochemical Society Transactions, 31:1491-1496, 2003.
17. D. Watts and S. Strogatz. Collective dynamics of small world networks. Nature, 393(6684):440-442, June 1998.
18. L. Wu, T. Hughes, A. Davierwala, M. Robinson, R. Stoughton, and S. Altschuler. Large-scale prediction of saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nature Genetics, 31:255-265, June 2002.
19. I. Xenarios, D. Rice, L. Salwinski, M. Baron, E. Marcotte, and D. Eisenberg. Dip: the database of interacting proteins. Nucl. Acids Res., 28(1):289-291, 2000.