GraMoFoNe: a Cytoscape plugin for querying motifs without topology in Protein-Protein Interactions networks
作者： Stéphane Vialette , Guillaume Blin , Florian Sikora
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摘要: During the last decade, data on Protein-Protein Interactions (PPI) has increased in a huge manner. Searching for motifs PPI Network thus became crucial problem to interpret this data. A large part of literature is devoted query with given topology. However, biological are, by now, so noisy (missing and erroneous information) that topology motif can be unrelevant. Consequently, Lacroix et al. (TCBB 2006) defined new problem, called GRAPH MOTIF, which consists searching multiset colors vertex-colored graph. In article, we present GraMoFoNe, plugin Cytoscape based Linear Pseudo-Boolean optimization solver handles MOTIF some its extensions.
archives-ouvertes.fr参考文章(24)
Guillaume Blin, Florian Sikora, Stéphane Vialette, Querying Protein-Protein Interaction Networks international symposium on bioinformatics research and applications. ,vol. 5542, pp. 52- 62 ,(2009) , 10.1007/978-3-642-01551-9_6
Michael R. Fellows, Guillaume Fertin, Danny Hermelin, Stéphane Vialette, Sharp Tractability Borderlines for Finding Connected Motifs in Vertex-Colored Graphs Automata, Languages and Programming. pp. 340- 351 ,(2007) , 10.1007/978-3-540-73420-8_31
Riccardo Dondi, Guillaume Fertin, Stéphane Vialette, Maximum Motif Problem in Vertex-Colored Graphs combinatorial pattern matching. ,vol. 5577, pp. 221- 235 ,(2009) , 10.1007/978-3-642-02441-2_20
Nadja Betzler, Michael R. Fellows, Christian Komusiewicz, Rolf Niedermeier, Parameterized Algorithms and Hardness Results for Some Graph Motif Problems combinatorial pattern matching. ,vol. 5029, pp. 31- 43 ,(2008) , 10.1007/978-3-540-69068-9_6
Laurie Issel-Tarver, Karen R. Christie, Kara Dolinski, Rey Andrada, Rama Balakrishnan, Catherine A. Ball, Gail Binkley, Stan Dong, Selina S. Dwight, Dianna G. Fisk, Midori Harris, Mark Schroeder, Anand Sethuraman, Kane Tse, Shuai Weng, David Botstein, J. Michael Cherry, Saccharomyces Genome Database. Methods in Enzymology. ,vol. 350, pp. 329- 346 ,(2002) , 10.1016/S0076-6879(02)50972-1
Alexander Schrijver, Theory of Linear and Integer Programming ,(1986)
Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan, QNet: a tool for querying protein interaction networks. Journal of Computational Biology. ,vol. 15, pp. 913- 925 ,(2008) , 10.1089/CMB.2007.0172
S Altschula, Warren Gisha, Webb Millerb, E Meyersc, D Lipmana, None, Basic Local Alignment Search Tool Journal of Molecular Biology. ,vol. 215, pp. 403- 410 ,(1990) , 10.1016/S0022-2836(05)80360-2
M. Pellegrini, E. M. Marcotte, M. J. Thompson, D. Eisenberg, T. O. Yeates, Assigning protein functions by comparative genome analysis protein phylogenetic profiles Proceedings of the National Academy of Sciences of the United States of America. ,vol. 96, pp. 4285- 4288 ,(2000) , 10.1073/PNAS.96.8.4285
Peter Uetz, Loic Giot, Gerard Cagney, Traci A Mansfield, Richard S Judson, James R Knight, Daniel Lockshon, Vaibhav Narayan, Maithreyan Srinivasan, Pascale Pochart, Alia Qureshi-Emili, Ying Li, Brian Godwin, Diana Conover, Theodore Kalbfleisch, Govindan Vijayadamodar, Meijia Yang, Mark Johnston, Stanley Fields, Jonathan M Rothberg, None, A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae Nature. ,vol. 403, pp. 623- 627 ,(2000) , 10.1038/35001009