A Collective NMF method for detecting protein functional module from multiple data sources

2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012

Volumn , Issue , 2012, Pages 655-660

  Zhang, Yuan ^a   Du, Nan ^b   Ge, Liang ^b   Jia, Kebin ^a   Zhang, Aidong ^b  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

Algorithm

Indexed keywords

ADJACENCY MATRICES; BIOLOGICAL DATA; CLUSTERING RESULTS; COMMON FACTORS; DATA-SOURCES; DETECTION PERFORMANCE; FUNCTIONAL MODULES; FUSION METHODS; GENE EXPRESSION DATA; GENE ONTOLOGY; HIGH THROUGHPUT EXPERIMENTS; MATRIX FACTORIZATIONS; MULTIPLE DATA SOURCES; NONNEGATIVE MATRIX FACTORIZATION; PROTEIN-PROTEIN INTERACTION NETWORKS; SOFT CLUSTERING; TWO-GRAPHS;

ALGORITHMS; CLUSTERING ALGORITHMS; FACTORIZATION; GENE EXPRESSION; MATRIX ALGEBRA; PROTEINS; THROUGHPUT;

BIOINFORMATICS;

EID: 84869478245     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2382936.2383053     Document Type: Conference Paper

References (27)

1. Gary D Bader and Christopher Wv Hogue. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics, 4(1):2, 2003.
2. Rachel B Brem and Leonid Kruglyak. The landscape of genetic complexity across 5,700 gene expression traits in yeast. Proceedings of the National Academy of Sciences of the United States of America, 102(5):1572-1577, 2005.
3. Yanhua Chen, Manjeet Rege, Ming Dong, and Jing Hua. Non-negative matrix factorization for semi-supervised data clustering. Knowledge and Information Systems, 17(3):355-379, 2008.
4. Young-rae Cho, Woochang Hwang, and Aidong Zhang. Efficient modularization of weighted protein interaction networks using k-hop graph reduction. BioInformatics and BioEngineering 2006 BIBE 2006 Sixth IEEE Symposium on, pages 289-298, 2006.
5. Young-Rae Cho, Lei Shi, and Aidong Zhang. Flownet: Flow-based approach for efficient analysis of complex biological networks. 2009 Ninth IEEE International Conference on Data Mining, pages 91-100, 2009.
6. Karthik Devarajan. Nonnegative matrix factorization: An analytical and interpretive tool in computational biology. PLoS Computational Biology, 4(7):12, 2008.
7. Chris Ding, Xiaofeng He, and Horst D Simon. On the equivalence of nonnegative matrix factorization and spectral clustering. Proc SIAM Data Mining Conf, 44(4):606â ǍŞ610, 2005.
8. Xiaoli Zhang Fern and Carla E Brodley. Solving cluster ensemble problems by bipartite graph partitioning. Twentyfirst international conference on Machine learning ICML 04, pages 36-41, 2004.
9. A C Gavin, P Aloy, P Grandi, R Krause, M Boesche, M Marzioch, C Rau, L J Jensen, S Bastuck, B Dumpelfeld, and et al. Proteome survey reveals modularity of the yeast cell machinery. Nature, 440(7084):631-636, 2006.
10. M Girvan and M E J Newman. Community structure in social and biological networks. Proceedings of the National Academy of Sciences of the United States of America, 99(12):7821-7826, 2002.
11. Hyunsoo Kim and Haesun Park. Nonnegative matrix factorization based on alternating nonnegativity constrained least squares and active set method. SIAM Journal on Matrix Analysis and Applications, 30(2):713, 2008.
12. Jingu Kim and Haesun Park. Sparse nonnegative matrix factorization for clustering. Science, pages 1-15, 2006.
13. Nevan J Krogan, Gerard Cagney, Haiyuan Yu, Gouqing Zhong, Xinghua Guo, Alexandr Ignatchenko, Joyce Li, Shuye Pu, Nira Datta, Aaron P Tikuisis, and et al. Global landscape of protein complexes in the yeast saccharomyces cerevisiae. Nature, 440(7084):637-643, 2006.
14. D D Lee and H S Seung. Learning the parts of objects by non-negative matrix factorization. Nature, 401(6755):788-91, 1999.
15. Chuan Lin, Young-rae Cho, Woo-chang Hwang, Pengjun Pei, and Aidong Zhang. Clustering methods in protein-protein interaction network. in Knowledge Discovery in Bioinformatics Techniques Methods and Application, 2006.
16. Dekang Lin. An information-theoretic definition of similarity. Quality, 1:296-304, 1998.
17. M E J Newman. Finding community structure in networks using the eigenvectors of matrices. Physical Review E - Statistical, Nonlinear and Soft Matter Physics, 74(3 Pt 2):036104, 2006.
18. J-P Onnela, J SaramÃd'ki, J HyvÃu″nen, G SzabÃş, D Lazer, K Kaski, J Kert Ãl'sz, and A-L Barabà a̧si. Structure and tie strengths in mobile communication networks. Proceedings of the National Academy of Sciences of the United States of America, 104(18):7332-7336, 2007.
19. Max Planck and Ulrike Von Luxburg. A tutorial on spectral clustering a tutorial on spectral clustering. Statistics and Computing, 17(August):395-416, 2006.
20. Shuye Pu, Jessica Wong, Brian Turner, Emerson Cho, and Shoshana J Wodak. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Research, 37(3):825-831, 2009.
21. Seung Yon Rhee, Valerie Wood, Kara Dolinski, and Sorin Draghici. Use and misuse of the gene ontology annotations. Nature Reviews Genetics, 9(7):509-515, 2008.
22. B Schwikowski, P Uetz, and S Fields. A network of protein-protein interactions in yeast. Nature Biotechnology, 18(12):1257-1261, 2000.
23. Alexander J Smola and Risi Kondor. Kernels and regularization on graphs. Machine Learning, 2777:1-15, 2003.
24. Alexander Strehl and Joydeep Ghosh. Cluster ensemblesa knowledge reuse framework for combining multiple partitions. Journal of Machine Learning Research, 3(3):583-617, 2003.
25. Christian Von Mering, Roland Krause, Berend Snel, Michael Cornell, Stephen G Oliver, Stanley Fields, and Peer Bork. Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417(6887):399-403, 2002.
26. Jianxin Wang, Min Li, Jianer Chen, and Yi Pan. A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks. IEEEACM Transactions on Computational Biology and Bioinformatics, 8(3):607-620, 2011.
27. R Wang, S Zhang, Y Wang, X Zhang, and L Chen. Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures. Neurocomputing, 72(1-3):134-141, 2008.