Functional Alignment of Metabolic Networks

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• 作者：Arnon Mazza (5)
  Allon Wagner (5) (6)
  Eytan Ruppin (5) (7) (8)
  Roded Sharan (5)
  
  5. Blavatnik School of Computer Science ; Tel Aviv University ; 69978 ; Tel Aviv ; Israel
  6. Department of Electrical Engineering and Computer Science ; University of California ; Berkeley ; CA ; 94720-1770 ; USA
  7. The Sackler School of Medicine ; Tel Aviv University ; 69978 ; Tel Aviv ; Israel
  8. Department of Computer Science ; Institute of Advanced Computer Sciences (UMIACS) & the Center for Bioinformatics and Computational Biology ; University of Maryland ; College Park ; MD ; 20742 ; USA
  
• 刊名：Lecture Notes in Computer Science
• 出版年：2015
• 出版时间：2015
• 年：2015
• 卷：9029
• 期：1
• 页码：243-255
• 全文大小：227 KB
• 参考文献：1. Sharan, R, Suthram, S, Kelley, RM, Kuhn, T, McCuine, S, Uetz, P, Sittler, T, Karp, RM, Ideker, T (2005) Conserved patterns of protein interaction in multiple species. Proceedings of the National Academy of Sciences of the United States of America 102: pp. 1974-1979 CrossRef
  2. Ogata, H, Fujibuchi, W, Goto, S, Kanehisa, M (2000) A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. Nucleic Acids Research 28: pp. 4021-4028 CrossRef
  3. Kelley, BP, Sharan, R, Karp, RM, Sittler, T, Root, DE, Stockwell, BR, Ideker, T (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proceedings of the National Academy of Sciences of the United States of America 100: pp. 11394-9 CrossRef
  4. Flannick, J, Novak, A, Srinivasan, BS, McAdams, HH, Batzoglou, S (2006) Graemlin: general and robust alignment of multiple large interaction networks. Genome Research 16: pp. 1169-1181 CrossRef
  5. Zhenping, L., Zhang, S., Wang, Y., Zhang, X.S., Chen, L.: Alignment of molecular networks by integer quadratic programming. Bioinformatics (Oxford, England) 23(13), 1631鈥?639 (2007)
  6. Singh, R, Xu, J, Berger, B (2008) Global alignment of multiple protein interaction networks with application to functional orthology detection. Proceedings of the National Academy of Sciences of the United States of America 105: pp. 12763-8 CrossRef
  7. Pinter, RY, Rokhlenko, O, Yeger-lotem, E, Ziv-ukelson, M (2005) Alignment of metabolic pathways. Bioinformatics 21: pp. 3401-3408 CrossRef
  8. Li, Y., de Ridder, D., de Groot, M.J., Reinders, M.J.: Metabolic pathway alignment (M-Pal) reveals diversity and alternatives in conserved networks. In: Advances in Bioinformatics and Computational Biology, vol. 6, pp. 273鈥?85. Imperial College Press (2008)
  9. Ay, F, Kellis, M, Kahveci, T (2011) SubMAP: aligning metabolic pathways with subnetwork mappings. Journal of Computational Biology 18: pp. 219-235 CrossRef
  10. Abaka, G, Biyikoglu, T, Erten, C (2013) CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways. Bioinformatics 29: pp. i145-i153 CrossRef
  11. Baldan, P., Cocco, N., Simeoni, M.: Comparison of metabolic pathways by considering potential fluxes. In: BioPPN 2012: 3rd International Workshop on Biological Processes and Petri Nets, 2鈥?7 (2012)
  12. Schuster, S., Hilgetag, C.: On elementary flux modes in biochemical reaction systems at steady state. Journal of Biological Systems 2(2), 165鈥?82 (1994)
  13. Ay, F., Kahveci, T.: Functional similarities of reaction sets in metabolic pathways. In: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, BCB 2010, pp. 102鈥?11 (2010)
  14. Orth, JD, Thiele, I, Palsson, BO (2010) What is flux balance analysis?. Nature Biotechnology 28: pp. 245-248 CrossRef
  15. Feist, AM, Palsson, BO (2010) The biomass objective function. Current Opinion in Microbiology 13: pp. 344-349 CrossRef
  16. Mahadevan, R., Schilling, C.: The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5(4), 264鈥?76 (2003)
  17. Mo, ML, Palsson, BO, Herrg氓rd, MJ (2009) Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Systems Biology 3: pp. 37 CrossRef
  18. Burgard, AP, Nikolaev, EV, Schilling, CH, Maranas, CD (2004) Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14: pp. 301-312 CrossRef
  19. Munkres, J (1957) Algorithms for the assignment and transportation problems. Journal of the Society for Industrial and Applied Mathematics 5: pp. 32-38 CrossRef
  20. Bilu, Y, Shlomi, T, Barkai, N, Ruppin, E (2006) Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states. PLoS Comput. Biol. 2: pp. e106 CrossRef
  21. Guimer脿, R, Sales-Pardo, M, Amaral, LAN (2007) A network-based method for target selection in metabolic networks. Bioinformatics 23: pp. 1616-22 CrossRef
  22. Liao, CS, Lu, K, Baym, M, Singh, R, Berger, B (2009) IsoRankN: spectral methods for global alignment of multiple protein networks. Bioinformatics 25: pp. i253-8 CrossRef
  23. Feist, AM, Henry, CS, Reed, JL, Krummenacker, M, Joyce, AR, Karp, PD, Broadbelt, LJ, Hatzimanikatis, V, Palsson, BO (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Systems Biology 3: pp. 121
  24. Orth, J.D., Conrad, T.M., Na, J., Lerman, J.A., Nam, H., Feist, A.M., Palsson, B.O.: A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Molecular Systems Biology 7(535), 535 (2011)
  25. Duarte, N.C., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R., Palsson, B.O.: Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences of the United States of America 104(6), 1777鈥?782 (2007)
  26. Resnik, P (1999) Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language. Journal of Artificial Intelligence Research 11: pp. 95-130
  27. Amberger, J, Bocchini, CA, Scott, AF, Hamosh, A (2009) McKusick鈥檚 Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Research 37: pp. D793-D796 CrossRef
  28. Mosharov, E, Cranford, MR, Banerjee, R (2000) The quantitatively important relationship between homocysteine metabolism and glutathione synthesis by the transsulfuration pathway and its regulation by redox changes. Biochemistry 39: pp. 13005-13011 CrossRef
  29. Robert, K, Nehm茅, J, Bourdon, E, Pivert, G, Friguet, B, Delcayre, C, Delabar, J, Janel, N (2005) Cystathionine $$\beta $$ synthase deficiency promotes oxidative stress, fibrosis, and steatosis in mice liver. Gastroenterology 128: pp. 1405-1415 CrossRef
  
• 作者单位：Research in Computational Molecular Biology
• 丛书名：978-3-319-16705-3
• 刊物类别：Computer Science
• 刊物主题：Artificial Intelligence and Robotics
  Computer Communication Networks
  Software Engineering
  Data Encryption
  Database Management
  Computation by Abstract Devices
  Algorithm Analysis and Problem Complexity
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1611-3349

文摘

Network alignment has become a standard tool in comparative biology, allowing the inference of protein function, interaction and orthology. However, current alignment techniques are based on topological properties of networks and do not take into account their functional implications. Here we propose, for the first time, an algorithm to align two metabolic networks by taking advantage of their coupled metabolic models. These models allow us to assess the functional implications of genes or reactions, captured by the metabolic fluxes that are altered following their deletion from the network. Such implications may spread far beyond the region of the network where the gene or reaction lies. We apply our algorithm to align metabolic networks from various organisms, ranging from bacteria to humans, showing that our alignment can reveal functional orthology relations that are missed by conventional topological alignments.