The Community for Technology Leaders
RSS Icon
Issue No.04 - October-December (2010 vol.7)
pp: 628-635
Guillaume Blin , Université Paris-Est, France
Florian Sikora , Université Paris-Est, France
Stéphane Vialette , Université Paris-Est, France
Recent techniques increase rapidly the amount of our knowledge on interactions between proteins. The interpretation of these new information depends on our ability to retrieve known substructures in the data, the Protein-Protein Interactions (PPIs) networks. In an algorithmic point of view, it is an hard task since it often leads to NP-hard problems. To overcome this difficulty, many authors have provided tools for querying patterns with a restricted topology, i.e., paths or trees in PPI networks. Such restriction leads to the development of fixed parameter tractable (FPT) algorithms, which can be practicable for restricted sizes of queries. Unfortunately, Graph Homomorphism is a W[1]-hard problem, and hence, no FPT algorithm can be found when patterns are in the shape of general graphs. However, Dost et al. [2] gave an algorithm (which is not implemented) to query graphs with a bounded treewidth in PPI networks (the treewidth of the query being involved in the time complexity). In this paper, we propose another algorithm for querying pattern in the shape of graphs, also based on dynamic programming and the color-coding technique. To transform graphs queries into trees without loss of informations, we use feedback vertex set coupled to a node duplication mechanism. Hence, our algorithm is FPT for querying graphs with a bounded size of their feedback vertex set. It gives an alternative to the treewidth parameter, which can be better or worst for a given query. We provide a python implementation which allows us to validate our implementation on real data. Especially, we retrieve some human queries in the shape of graphs into the fly PPI network.
Graph query, pattern matching, dynamic programming, protein-protein interactions networks.
Guillaume Blin, Florian Sikora, Stéphane Vialette, "Querying Graphs in Protein-Protein Interactions Networks Using Feedback Vertex Set", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, no. 4, pp. 628-635, October-December 2010, doi:10.1109/TCBB.2010.53
[1] G. Blin, F. Sikora, and S. Vialette, "Querying Protein-Protein Interaction Networks," Proc. Fifth Int'l Symp. Bioinformatics Research and Applications (ISBRA '09), S. Istrail, P. Pevzner, and M. Waterman, eds., pp. 52-62, May 2009.
[2] B. Dost, T. Shlomi, N. Gupta, E. Ruppin, V. Bafna, and R. Sharan, "QNet: A Tool for Querying Protein Interaction Networks," Proc. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 1-15, 2007.
[3] A. Gavin et al., "Functional Organization of the Yeast Proteome by Systematic Analysis of Protein Complexes," Nature, vol. 414, no. 6868, pp. 141-147, 2002.
[4] Y. Ho et al., "Systematic Identification of Protein Complexes in Saccharomyces Cerevisae by Mass Spectrometry," Nature, vol. 415, no. 6868, pp. 180-183, 2002.
[5] P. Uetz et al., "A Comprehensive Analysis of Protein-Protein Interactions in Saccharomyces Cerevisae," Nature, vol. 403, no. 6770, pp. 623-627, 2000.
[6] T. Reguly et al., "Comprehensive Curation and Analysis of Global Interaction Networks in Saccharomyces Cerevisiae," J. Biology, vol. 5, no. 4, 2006.
[7] M. Pellegrini, E. Marcotte, M. Thompson, D. Eisenberg, and T. Yeates, "Assigning Protein Functions by Comparative Genome Analysis: Protein Phylogenetic Profiles," Proc. Nat'l Academy of Sciences USA, vol. 96, no. 8, pp. 4285-4288, 1999.
[8] M. Garey and D. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman, 1979.
[9] B. Kelley, R. Sharan, R. Karp, T. Sittler, D.E. Root, B. Stockwell, and T. Ideker, "Conserved Pathways within Bacteria and Yeast as Revealed by Global Protein Network Alignment," Proc. Nat'l Academy of Sciences USA, vol. 100, no. 20, pp. 11394-11399, 2003.
[10] T. Shlomi, D. Segal, E. Ruppin, and R. Sharan, "QPath: A Method for Querying Pathways in a Protein-Protein Interaction Network," BMC Bioinformatics, vol. 7, article no. 199, 2006.
[11] N. Alon, R. Yuster, and U. Zwick, "Color Coding," J. ACM, vol. 42, no. 4, pp. 844-856, 1995.
[12] R. Downey and M. Fellows, Parameterized Complexity. Springer-Verlag, 1999.
[13] R. Pinter, O. Rokhlenko, E. Yeger-Lotem, and M. Ziv-Ukelson, "Alignment of Metabolic Pathways," Bioinformatics, vol. 21, no. 16, pp. 3401-3408, 2005.
[14] H. Bodlaender, "A Tourist Guide through Treewidth," Acta Cybernetica, vol. 11, pp. 1-23, 1993.
[15] S. Arnborg, D. Corneil, and A. Proskurowski, "Complexity of Finding Embeddings in a $k$ -Tree," J. Algebraic and Discrete Methods, vol. 8, no. 2, pp. 277-284, 1987.
[16] Q. Cheng, P. Berman, R. Harrison, and A. Zelikovsky, "Fast Alignments of Metabolic Networks," Proc. 2008 IEEE Int'l Conf. Bioinformatics and Biomedicine, pp. 147-152, 2008.
[17] R. Karp, "Reducibility among Combinatorial Problems," Complexity of Computer Computations, J. Thatcher and R. Miller, eds., pp. 85-103, Plenum Press, 1972.
[18] J. Guo, J. Gramm, F. Hüffner, R. Niedermeier, and S. Wernicke, "Compression-Based Fixed-Parameter Algorithms for Feedback Vertex Set and Edge Bipartization," J. Computer and System Sciences, vol. 72, no. 8, pp. 1386-1396, 2006.
[19] S. Thomasse, "A Quadratic Kernel for Feedback Vertex Set," Proc. 19th Ann. ACM-SIAM Symp. Discrete Algorithms, 2009.
[20] S. Altschul, W. Gish, W. Miller, E. Myers, and D. Lipman, "Basic Local Alignment Search Tool," J. Molecular Biology, vol. 215, no. 3, pp. 403-410, 1990.
[21] J. Scott, T. Ideker, R. Karp, and R. Sharan, "Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks," J. Computational Biology, vol. 13, pp. 133-144, 2006.
[22] S. Bruckner, F. Hüffner, R. Karp, R. Shamir, and R. Sharan, "Topology-Free Querying of Protein Interaction Networks," Proc. 13th Ann. Int'l Conf. Computational Molecular Biology (RECOMB), pp. 74-89, 2009.
[23] H. Bodlaender and A. Koster, "Combinatorial Optimization on Graphs of Bounded Treewidth," The Computer J., vol. 51, no. 3, pp. 255-269, 2007.
[24] I. Xenarios, L. Salwinski, X. Duan, P. Higney, S. Kim, and D. Eisenberg, "DIP, the Database of Interacting Proteins: A Research Tool for Studying Cellular Networks of Protein Interactions," Nucleic Acids Research, vol. 30, no. 1, pp. 303-305, 2002.
[25] P. Dent, A. Yacoub, P. Fisher, M. Hagan, and S. Grant, "MAPK Pathways in Radiation Responses," Oncogene, vol. 22, pp. 5885-5896, 2003.
[26] M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, and M. Hattori, "The KEGG Resource for Deciphering the Genome," Nucleic Acids Research, vol. 32, pp. 277-280, 2004.
[27] F. Huffner, S. Wernicke, and T. Zichner, "Algorithm Engineering for Color-Coding to Facilitate Signaling Pathway Detection," Proc. Fifth Asia-Pacific Bioinformatics Conf., 2007.
[28] M. Fellows, "Parameterized Complexity: New Developments and Research Frontiers," Proc. New Zealand Math. Sciences Research Inst. Summer Workshop, pp. 51-72, 2001.
[29] V. Lacroix, C. Fernandes, and M.-F. Sagot, "Motif Search in Graphs: Application to Metabolic Networks," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 360-368, Oct.-Dec. 2006.
[30] M. Fellows, G. Fertin, D. Hermelin, and S. Vialette, "Sharp Tractability Borderlines for Finding Connected Motifs in Vertex-Colored Graphs," Proc. 34th Int'l Colloquium Automata, Languages and Programming (ICALP), pp. 340-351, 2007.
[31] N. Betzler, M. Fellows, C. Komusiewicz, and R. Niedermeier, "Parameterized Algorithms and Hardness Results for Some Graph Motif Problems," Proc. 19th Ann. Symp. Combinatorial Pattern Matching (CPM), pp. 31-43, 2008.
[32] R. Dondi, G. Fertin, and S. Vialette, "Weak Pattern Matching in Colored Graphs: Minimizing the Number of Connected Components," Proc. 10th Italian Conf. Theoretical Computer Science (ICTCS), pp. 27-38, 2007.
[33] R. Dondi, G. Fertin, and S. Vialette, "Maximum Motif Problem in Vertex-Colored Graphs," Proc. 20th Ann. Symp. Combinatorial Pattern Matching (CPM '09), G. Kucherov and E. Ukkonen, eds., pp. 221-235, 2009.
[34] G. Blin, F. Sikora, and S. Vialette, "GraMoFoNe: A Cytoscape Plugin for Querying Motifs without Topology in Protein-Protein Interactions Networks," Proc. Second Int'l Conf. Bioinformatics and Computational Biology (BICoB-2010), pp. 38-43, 2010.
[35] S. Schbath, V. Lacroix, and M. Sagot, "Assessing the Exceptionality of Coloured Motifs in Networks," EURASIP J. Bioinformatics and Systems Biology, vol. 2009, pp. 1-10, 2009.
16 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool