Function prediction using neighborhood patterns

8th International Workshop on Data Mining in Bioinformatics, BIOKDD 2008 - Held in conjunction with SIGKDD conference, KDD 2008

Volumn , Issue , 2008, Pages 4-10

  Bogdanov, Petko ^a   Singh, Ambuj ^a  

^a University of California   (United States)

Author keywords

Classification; Feature Extraction; Protein Function Prediction; Protein Interaction Network

Indexed keywords

BIOINFORMATICS; CLASSIFICATION (OF INFORMATION); ECONOMIC AND SOCIAL EFFECTS; FORECASTING;

FEATURES EXTRACTION; FUNCTION PREDICTION; HIGH-THROUGHPUT METHOD; INTERACTION NETWORKS; LARGE AMOUNTS; NEIGHBORHOOD PATTERN; NEIGHBOURHOOD; PROTEIN FUNCTION PREDICTION; PROTEIN INTERACTION; PROTEIN INTERACTION NETWORKS;

PROTEINS;

EID: 84977933919     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (24)

1. Biogrid: General repository for interaction datasets. http://www.thebiogrid.org/, 2006.
2. V. Arnau, S. Mars, and I. Marin. Iterative clustering analysis of protein interaction data. Bioinformatics, 2005.
3. Z. Barutcuoglu, R. Schapire, and O. Troyanskaya. Hierarchical multi-label prediction of gene function. Bioinformatics, 2006.
4. C. Brun, F. Chevenet, D. Martin, J. Wojcik, A. Guenoche, and B. Jacq. Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network. Genome Biology, 5:R6, 2003.
5. T. Can, O. Camoglu, and A. K. Singh. Analysis of protein interaction networks using random walks. Proceedings of the 5th ACM SIGKDD Workshop on Data Mining in Bioinformatics, 2005.
6. J. Chen, W. Hsu, M. L. Lee, and S.-K. Ng. Labeling network motifs in protein interactomes for protein function prediction. ICDE, 2007.
7. H. Chua, W. Sung, and L. Wong. Exploiting indirect neighbors and topological weight to predict protein function from protein-protein interactions. Bioinformatics, 2006.
8. H. Chua, W. Sung, and L. Wong. Using indirect protein interactions for the prediction of gene ontology functions. BMC Bioinformatics, 2007.
9. Y. G. Database. http://www.yeastgenome.org/.
10. R. Dunn, F. Dudbridge, and C. Sanderson. The use of edge-betweenness clustering to investigate the biological function in protein interaction networks. BMC Bioinformatics, 2005.
11. T. gene ontology consortium. Gene ontology: Tool for the unification of biology. Nature, 2000.
12. J. Han, N. Bertin, and T. H. et Al. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 2004.
13. H. Hishigaki, K. Nakai, T. Ono, A. Tanigami, and T. Takagi. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast, 2001.
14. U. Karaoz, T. M. Murali, S. Letovsky, Y. Zheng, C. Ding, C. R. Cantor, and S. Kasif. Whole-genome annotation by using evidence integration in functional-linkage networks. PNAS, 101:2888-2893, 2004.
15. S. Letovsky and S. Kasif. Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics, 19:i197-i204, 2003.
16. K. Maciag, S. Altschuler, M. Slack, N. Krogan, A. Emili, J. Greenblatt, T. Maniatis, and L. Wu. Systems-level analyses identify extensive coupling among gene expression machines. Molecular Systems Biology, 2006.
17. C. V. Mering, M. Huynen, D. Jaeggi, S. Schmidt, P. Bork, and B. Snel. String: a database of predicted functional associations between proteins. Nucleic Acids Res., 2003.
18. H. W. Mewes, D. Frishman, U. Guldener, G. Mannhaupt, K. Mayer, M. Mokrejs, B. Morgenstern, M. Munsterkotter, S. Rudd, and B. Weil. Mips: a database for genomes and protein sequences. Nucleic Acids Res., 30:31-34, 2002.
19. E. Nabieva, K. Jim, A. Agarwal, B. Chazelle, and M. Singh. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics, 21:i302-i310, 2005.
20. M. P. Samanta and S. Liang. Predicting protein functions from redundancies in large-scale protein interaction networks. PNAS, 100:12579-12583, 2003.
21. B. Schwikowski, P. Uetz, and S. Fields. A network of protein-protein interactions in yeast. Nature, 2000.
22. R. Sharan, I. Ulitsky, and R. Shamir. Network-based prediction of protein function. Molecular Systems Biology, 2007.
23. V. Spirin and L. Mirny. Protein complexes and functional modules in molecular networks. PNAS, 2003.
24. G. X. Yu, E. M. Glass, N. T. Karonis, and N. Maltsev. Knowledge-based voting algorithm for automated protein functional annotation. PROTEINS: Structure, Function, and Bioinformatics, 61:907-917, 2005.