A cytoscape based framework for efficient sub-graph isomorphic protein-protein interaction motif lookup

Proceedings of the ACM Symposium on Applied Computing

Volumn , Issue , 2010, Pages 1572-1576

  Amin, Mohammad Shafkat ^a   Bhattacharjee, Anupam ^a   Jamil, Hasan ^a  

^a Wayne State University   (United States)

Author keywords

Cytoscape plugin; protein protein interaction network; subgraph isomorphism

Indexed keywords

COMPUTATION METHODS; GAIN INSIGHT; LOOKUPS; ONLINE INTERACTION; PLUG-INS; PROTEIN-PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTIONS; QUERY NETWORKS; REAL-LIFE APPLICATIONS; STAND ALONE TOOLS; SUB-NETWORK; SUBGRAPH ISOMORPHISM; SUBGRAPHS; SUBNETWORKS;

ACTIVE NETWORKS; ONTOLOGY; SET THEORY;

PROTEINS;

EID: 77954706275     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1774088.1774424     Document Type: Conference Paper

References (19)

1. M. S. Amin, A. Bhattacharjee, and H. Jamil. A cytoscape based framework for efficient sub-graph isomorphism detection in protein-protein interaction network. Technical report, (http://integra.cs.wayne.edu), Wayne State University, 2009.
2. M. De Santo, P. Foggia, C. Sansone, and M. Vento. A large database of graphs and its use for benchmarking graph isomorphism algorithms. Pattern Recogn. Lett., 24(8):1067-1079, 2003.
3. A. Ferro, R. Giugno, G. Pigola, A. Pulvirenti, D. Skripin, G. D. D. Bader, and D. Shasha. Netmatch: a cytoscape plugin for searching biological networks. Bioinformatics, 2007.
4. M. R. Garey and D. S. Johnson. Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman & Co., New York, NY, USA, 1979.
5. H. Hishigaki, K. Nakai, T. Ono, A. Tanigami, and T. Takagi. Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast, 18:523-531, 2001.
6. H. Jamil. A novel knowledge representation framework for computing sub-graph isomorphic queries in interaction network databases. In IEEE International Conference on Tools with Artificial Intelligence, 2009.
7. H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A.-L. Barabási. The large-scale organization of metabolic networks. Nature, 407:823-826, October 2000.
8. M. Koyuturk, Y. Kim, S. Subramanium, W. Szpankowski, and A. Grama. Detecting conserved interaction patterns in biological networks. Journal of Computational Biology, 3(7):1299-1322, 2006. (Pubitemid 46100695)
9. M. Lappe and L. Holm. Algorithms for protein interaction networks. Biochemical Society Transactions, 33(3).
10. M. E. J. Newman. The structure and function of complex networks. SIAM Review, 45:167, 2003.
11. L. P. Cordella, P. Foggia, C. Sansone, and M. Vento. A (sub)graph isomorphism algorithm for matching large graphs. IEEE Trans. Pattern Anal. Mach. Intell., 26:1367-1372, 2004.
12. F. Schreiber and H. Schwöbbermeyer. Mavisto: a tool for the exploration of network motifs. Bioinformatics, 21:3572-3574, 2005.
13. K. Schrick, B. Garvik, and L. Hartwell. Mating in Saccharomyces cerevisiae: The Role of the Pheromone Signal Transduction Pathway in the Chemotropic Response to Pheromone. Genetics, 147:19-32, 1997. (Pubitemid 27385534)
14. H. Shang, Y. Zhang, X. Lin, and J. X. Yu. Taming verification hardness: an efficient algorithm for testing subgraph isomorphism. PVLDB, 1:364-375, 2008.
15. P. Shannon, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research, 13(11):2498-2504, 2003.
16. J. R. Ullmann. An algorithm for subgraph isomorphism. J. ACM, 23(1):31-42, 1976.
17. S. Wernicke and F. Rasche. Fanmod: a tool for fast network motif detection. Bioinformatics, 22:1152-1153, 2006.
18. Yip, Y. Kevin, Yu, Haiyuan, Kim, M. Philip, Schultz, Martin, Gerstein, and Mark. The tyna platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks. Bioinformatics, 22:2968-2970, December 2006.
19. J. Yu, S. Pacifico, G. Liu, and R. Finley. Droid: the drosophila interactions database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics, 9(1):461+, 2008.