Large-scale protein-protein Interaction prediction using novel kernel methods

International Journal of Data Mining and Bioinformatics

Volumn 2, Issue 2, 2008, Pages 145-156

  Chen, Xue Wen ^a   Han, Bing ^a   Fang, Jianwen ^b   Haasl, Ryan J ^b  

^a University of Kansas   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

Bioinformatics; Data mining; Kernel method; PPIs; Protein protein interactions; Support vector machine; SVM

Indexed keywords

EID: 47149118685     PISSN: 17485673     EISSN: 17485681     Source Type: Journal    
DOI: 10.1504/IJDMB.2008.019095     Document Type: Article

References (28)

1. Aytuna, A.S., Gursoy, A. and Keskin, O. (2005) 'Prediction of protein-protein interactions by combining structure and sequence', Bioinformatics, Vol. 21, No. 12, pp.2850-2855.
2. Ben-Hur, A. and Noble, W.S. (2005) 'Kernel methods for predicting protein-protein interactions', Bioinformatics, Vol. 21, Suppl. 1, pp.i38-i46.
3. Bock, J. and Gough, D. (2001) 'Predicting protein-protein interactions from primary structure', Bioinformatics, Vol. 17, No. 5, pp.455-460.
4. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L.L., Studholme, D.J., Yeats, C. and Eddy, S.R. (2004) 'The Pfam protein families database', Nucleic Acids Res., Vol. 32, Database Issue, pp.D138-D141.
5. Burges, C.J.C. (1998) 'A tutorial on support vector machines for pattern recognition', Data Mining and Knowledge Discovery, Vol. 2, No. 2, pp.121-167.
6. Chen, X-w. and Liu, M. (2005) 'Prediction of protein-protein interactions using random decision forest framework', Bioinformatics Vol. 21, No. 24, pp.4394-4400.
7. Dandekar, T., Snel, B., Huynen, M. and Bork, P. (1998) 'Conservation of gene order: A fingerprint of proteins that physically interact', Trends in Biochemical Sciences, Vol. 23, No. 9, pp.324-328.
8. Deng, M., Mehta, S., Sun, F. and Chen, T. (2002) 'Inferring domain-domain interactions from protein-protein interactions', Genome Research, Vol. 12, No. 10, pp.1540-1548.
9. Enright, A.J., Iliopoulos, I., Kyrpides, N.C. and Ouzounis, C.A. (1999) 'Protein interaction maps for complete genomes based on gene fusion events', Nature, Vol. 402, No. 6757, pp.25, 26.
10. Fields, S. and Song, O-K. (1989) 'A novel genetic system to detect protein-protein interactions', Nature, Vol. 340, No. 6230, pp.245, 246.
11. Goh, C.S., Bogan, A.A., Joachimiak, M., Walther, D. and Cohen, F.E. (2000) 'Co-evolution of proteins with their interaction partners', J. Mol. Biol., Vol. 299, No. 2, pp.283-293.
12. Gomez, S.M., Noble, W.S. and Rzhetsky, A. (2003) 'Learning to predict protein-protein interactions from protein sequences', Bioinformatics Vol. 19, No. 15, pp.1875-1881.
13. Han, D., Kim, H., Seo, J. and Jang, W. (2003) 'A domain combination based probabilistic framework for protein-protein interaction prediction', Genome Inform., Vol. 14, pp.250-259.
14. Herbrich, R. (2001) Learning Kernel Classifiers: Theory and Algorithms, The MIT Press, Machachusetts.
15. Huynen, M., Snel, B., Lathe, W. and Bork, P. (2000) 'Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences', Genome Research, Vol. 10, No. 8, pp.1204-1210,
16. Jansen, R., Haiyuan, Y., Greenbaum, D., Kluger, Y., Krogan, N.J., Chung, S., Emili, A., Snyder, M., Greenblatt, J.F. and Gerstein, M. (2003) 'A bayesian networks approach for predicting protein-protein interactions from genomic data', Science, Vol. 302, No. 17, pp.449-453.
17. Jothi, R., Kann, M.G. and Przytycka, T.M. (2005) 'Predicting protein-protein interaction by searching evolutionary tree automorphism space', Bioinformatics, Vol. 21, Suppl. 1, pp.i241-i250.
18. Kim, W.K., Park, J. and Suh, J.K. (2002) 'Large scale statistical prediction of protein-protein interaction by potentially interacting domain (PID) pair', Genome Inform., Vol. 13, pp.42-50.
19. Li, H. and Tao, J. (2005) 'A class of edit kernels for SVMs to predict translation initiation sites in eukaryotic mRNAs', Journal of Computational Biology, Vol. 12, No. 6, pp.702-718.
20. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O. and Eisenberg, D. (1999) 'Detecting protein function and protein-protein interactions from genome sequences', Science, Vol. 285, No. 5428, pp.751-753.
21. Martin, S., Roe, D. and Faulon J-L. (2005) 'Predicting protein-protein interactions using signature products', Bioinformatics, Vol. 21, No. 2, pp.218-226.
22. Ng, S., Zhang, Z. and Tan, S. (2003) 'Integrative approach for computationally inferring protein domain interactions', Bioinformatics, Vol. 19, No. 8, pp.923-929.
23. Osuna, E., Freund, R. and Girosi, F. (1997) 'Support vector machines: training and applications', AI Memo 1602, Massachusetts Institute of Technology, Cambridge, MA.
24. Pazos, F., Helmer-Citterich, M., Ausiello, G. and Valencia, A. (1997) 'Correlated mutation contain information about protein-protein interaction', J. Mol. Biol., Vol. 271, No. 4, pp.511-523.
25. Pazos, F. and Valencia, A. (2001) 'Similarity of phylogenetic trees as indicator of protein-protein interaction', Protein Eng., Vol. 14, No. 9, pp.609-614.
26. Platt, J. (1999) 'Fast training of support vector machines using sequential minimal optimization', Advances in Kernel Methods - Support Vector Learning, Chapter 11, MIT Press, Cambridge, MA, pp.185-208.
27. Wojcik, J. and Schachter, V. (2001) 'Protein-protein interaction map inference using interacting domain profile pairs', Bioinformatics, Vol. 17, Suppl. 1, pp.S296-S305.
28. Zien, A., Ratsch, G., Mika, S., Schölkopf, B., Lemmen, C., Smola, A., Lengauer, T. and Müller, K.R. (2000) 'Engineering support vector machine kernels that recognize translation initiation sites', Bioinformatics, Vol. 16, No. 9, pp.799-807.