Prediction of metabolic pathways from genome-scale metabolic networks

BioSystems

Volumn 105, Issue 2, 2011, Pages 109-121

  Faust, Karoline ^a   Croes, Didier ^b   van Helden, Jacques ^b  

^a VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^b UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Metabolic network representation; Metabolic pathway definition; Metabolic pathway prediction; Subgraph extraction

Indexed keywords

DATA SET; GENE EXPRESSION; GENOME; GRAPHICAL METHOD; LITERATURE REVIEW; METABOLISM; NETWORK ANALYSIS; PHYLOGENETICS; PREDICTION;

ARTICLE; GENOMICS; HUMAN; METABOLISM; PREDICTION; REACTION ANALYSIS; SYSTEMS BIOLOGY;

EID: 79960366540     PISSN: 03032647     EISSN: 18728324     Source Type: Journal    
DOI: 10.1016/j.biosystems.2011.05.004     Document Type: Article

References (90)

1. Adler P., Reimand J., Jänes J., Kolde R., Peterson H., Vilo J. KEGGanim: pathway animations for high-throughput data. Bioinformatics 2008, 24:588-590.
2. Antonov A., Dietmann S., Mewes H. KEGG spider: interpretation of genomics data in the context of the global gene metabolic network. Genome Biology 2008, 9.
3. Antonov A., Dietmann S., Wong P., Mewes H. TICL-a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics. FEBS Journal 2009, 276:2084-2094.
4. Arita M. Metabolic reconstruction using shortest paths. Simulation Practice and Theory 2000, 8:109-125.
5. Arita M. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Research 2003, 13:2455-2466.
6. Arita M. The metabolic world of Escherichia coli is not small. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:1543-1547.
7. Backes C., Keller A., Kuentzer J., Kneissl B., Comtesse N., Elnakady Y.A., Mller R., Meese E., Lenhof H.-P. GeneTrail-advanced gene set enrichment analysis. Nucleic Acids Research 2007, 102:W186-W192.
8. Becker S., Feist A., Mo M., Hannum G., Palsson B., Herrgard M. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nature Protocol 2007, 2:727-738.
9. Blum T., Kohlbacher O. Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks. Journal of Computational Biology 2008, 15:565-576.
10. Boyer F., Viari A. Ab initio reconstruction of metabolic pathways. Bioinformatics 2003, 19:ii26-ii34.
11. Brohée S., Faust K., Lima-Mendez G., Sand O., Janky R., Vanderstocken G., Deville Y., van Helden J. NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Research 2008, 36:W444-W451.
12. Caspi R., Foerster H., Fulcher C., Kaipa P., Krummenacker M., Latendresse M., Paley S., Rhee S., Shearer A., Tissier C., Walk T., Zhang P., Karp P. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research 2008, 36:D623-D631.
13. Centler, F., di Fenizio, P.S., Matsumaru, N., Dittrich, P., 2005. Chemical organizations in the central sugar metabolism of Escherichia coli. Modeling and Simulation in Science Engineering and Technology, Post-proceedings of ECMTB 2005.
14. Chou C.-H., Chang W.-C., Chiu C.-M., Huang C.-C., Huang H.-D. FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Research 2009, 37:W129-W134.
15. Christian N., May P., Kempa S., Handorf T., Ebenhöh O. An integrative approach towards completing genome-scale metabolic networks. Molecular BioSystems 2009, 5:1889-1903.
16. Clarke B. Stoichiometric network analysis. Cell Biophysics 1988, 12:237-253.
17. Croes D., Couche F., Wodak S., van Helden J. Metabolic pathfinding: inferring relevant pathways in biochemical networks. Nucleic Acids Research 2005, 33:W326-W330.
18. Croes D., Couche F., Wodak S., van Helden J. Inferring meaningful pathways in weighted metabolic networks. Journal of Molecular Biology 2006, 356:222-236.
19. Dahlquist K.D., Salomonis N., Vranizan K., Lawlor S., Conklin B. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature Genetics 2002, 31:19-20.
20. Davidsen T., Beck E., Ganapathy A., Montgomery R., Zafar N., Yang Q., Madupu R., Goetz P., Galinsky K., White O., Sutton G. The comprehensive microbial resource. Nucleic Acids Research 2010, 38:D340-D345.
21. de Figueiredo L., Podhorski A., Rubio A., Kaleta C., Beasley J., Schuster S., Planes F. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics 2009, 25:3158-3165.
22. DeJongh M., Formsma K., Boillot P., Gould J., Rycenga M., Best A. Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics 2007, 8:139.
23. DeRisi J., Iyer V., Brown P. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278:680-686.
24. Dittrich M., Klau G., Rosenwald A., Dandekar T., Müller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24:i223-i231.
25. Duarte N., Becker S., Jamshidi N., Thiele I., Mo M., Vo T., ad B.O., Palsson R.S. 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 2007, 104:1777-1782.
26. Dupont, P., Callut, J., Dooms, G., Monette, J.-N., Deville, Y., 2006. Relevant subgraph extraction from random walks in a graph. Research Report UCL/FSA/INGI RR 2006-07.
27. Ellis L., Gao J., Fenner K., Wackett L. The University of Minnesota pathway prediction system: predicting metabolic logic. Nucleic Acids Research 2008, 36:W427-W432.
28. Eppstein D. Finding the k shortest paths. SIAM Journal on Computing 1999, 28:652-673.
29. Faust K., Croes D., van Helden J. In response to " Can sugars be produced from fatty acids? A test case for pathway analysis tools" Bioinformatics 2009, 25:3202-3205.
30. Faust K., Croes D., van Helden J. Metabolic pathfinding using RPAIR annotation. Journal of Molecular Biology 2009, 388:390-414.
31. Faust K., Dupont P., Callut J., van Helden J. Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics 2010, 26:1211-1218.
32. Fell D., Wagner A. The small world of metabolism. Nature Metabolic Engineering 2000, 18:1121-1122.
33. Forst C., Schulten K. Evolution of metabolisms: a new method for the comparison of metabolic pathways using genomics information. Journal of Computational Biology 1999, 6:343-360.
34. Forst C., Schulten K. Phylogenetic analysis of metabolic pathways. Journal of Molecular Biology 2001, 52:471-489.
35. Gagneur J., Jackson D., Casari G. Hierarchical analysis of dependency in metabolic networks. Bioinformatics 2003, 19:1027-1034.
36. Gama-Castro S., Jiménez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., naloza Spinola M.P., Contreras-Moreira B., Segura-Salazar J., niz Rascado L.M., Martínez-Flores I., Salgado H., Bonavides-Martínez C., Abreu-Goodger C., Rodríguez-Penagos C., Miranda-Ríos J., Morett E., Merino E., Huerta A., no Quintanilla L.T., Collado-Vides J. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research 2008, 36.
37. Gerlee P., Lizana L., Sneppen K. Pathway identification by network pruning in the metabolic network of Escherichia coli. Bioinformatics 2009, 25:3282-3288.
38. Ginsburg H. Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium. Trends in Parasitology 2009, 25:37-43.
39. Goesmann A., Haubrock M., Meyer F., Kalinowski J., Giegerich R. PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics 2002, 18:124-129.
40. Green M., Karp P. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 2004, 5:76.
41. Guimerà R., Amaral L. Functional cartography of complex metabolic networks. Nature 2005, 433:895-900.
42. Heath A., Bennett G., Kavraki L. Finding Metabolic Pathways Using Atom Tracking. Bioinformatics 2010, 26:1548-1555.
43. Henry C., DeJongh M., Best A., Frybarger P., Linsay B., Stevens R. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nature Biotechnology 2010, 2:977-982.
44. Herréz A. Biomolecules in the computer: Jmol to the rescue. Biochemistry and Molecular Biology Education 2006, 34:255-261.
45. Huang S., Fraenkel E. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Science Signaling 2009, 6053:101-112.
46. Ideker T., Ozier O., Schwikowski B., Siegel A. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18:S233-S240.
47. Jaworska J., Dimitrov S., Nikolova N., Mekenyan O. Probabilistic assessment of biodegradatability based on metabolic pathways: CATABOL system. SAR and QSAR in Environmental Research 2002, 13:307-323.
48. Jeong H., Tombor B., Albert R., Oltvai Z., Barabási A.-L. The large-scale organization of metabolic networks. Nature 2000, 407:651-654.
49. Jimenez V., Marzal A. Computing the k shortest paths: a new algorithm and an experimental comparison. Lecture Notes in Computer Science-Proceedings of the 3rd International Workshop on Algorithm Engineering 1668 1999, 15-29.
50. Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T., Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Research 2008, 36:D480-D484.
51. Karp P., Paley S. Representations of metabolic knowledge: pathways. Proceedings International Conference on Intelligent Systems for Molecular Biology 1994, 2:203-211.
52. Karp P., Paley S., Krummenacker M., Latendresse M., Dale J., Lee T., Kaipa P., Gilham F., Spaulding A., Popescu L., Altman T., Paulsen I., Keseler I., Caspi R. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Briefings in Bioinformatics 2009, 2:40-79.
53. Karp, R., 1972. Reducibility among combinatorial problems. In: Miller, R.E., Thatcher, J.W. (Eds.), Complexity of Computer Computations. Plenum Press, pp. 85-103.
54. Klamt S., Haus U.-U., Theis F. Hypergraphs and cellular networks. PLoS Computational Biology 2009, 5:5.
55. Kotera M., Hattori M., Oh M.-A., Yamamoto R., Komeno T., Yabuzaki J., Tonomura K., Goto S., Kanehisa M. RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions. Genome Informatics 2004, 15:P062.
56. Kotera M., Okuno Y., Hattori M., Goto S., Kanehisa M. Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. Journal of the American Chemical Society 2004, 126:16487-16498.
57. Küffner R., Zimmer R., Lengauer T. Pathway analysis in metabolic databases via differential metabolic display. Bioinformatics 2000, 16:825-836.
58. Lacroix V., Cottret L., Thébault P., Sagot M. An introduction to metabolic networks and their structural analysis. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2008, 5:594-617.
59. Lima-Mendez G., van Helden J. The powerful law of the power law and other myths in network biology. Molecular BioSystems 2009, 5:1482-1493.
60. Liu B., Pop M. Identifying differentially abundant metabolic pathways in metagenomic datasets. Lecture Notes in Computer Science: Bioinformatics Research and Applications 2010, 6053:101-112.
61. Ljubić I., Weiskircher R., Pferschy U., Klau G.W., Mutzel P., Fischetti M. An algorithmic framework for the exact solution of the prize-collecting Steiner Tree problem. Mathematical Programming Series B 2006, 105:427-449.
62. Ma H., Zeng A.-P. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19:270-277.
63. Mithani A., Preston G.M., Hein J. Hypergraph based tool for metabolic pathway prediction and network comparison. Bioinformatics 2009, 25:1831-1832.
64. Moriya Y., Itoh M., Okuda S., Yoshizawa A., Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Research 2007, 35:W182-W185.
65. Nelson D., Cox M. Lehninger Principles of Biochemistry 2005, fourth edition.
66. Noirel J., Ow S.Y., Sanguinetti G., Jaramillo A., Wright P.C. Automated extraction of meaningful pathways from quantitative proteomics data. Briefings in Functional Genomics and Proteomics 2008, 7:136-146.
67. Overbeek R., Disz T., Stevens R. The seed: a peer-to-peer environment for genome annotation. Communications of the ACM 2004, 47:47-51.
68. Paley S.M., Karp P.D. The pathway tools cellular overview diagram and Omics viewer. Nucleic Acids Research 2006, 34:3771-3778.
69. Pazos F., Guijas D., Valencia A., Lorenzo V.D. Metarouter: bioinformatics for bioremediation. Nucleic Acids Research 2005, 35:D588-D592.
70. Pitkänen E., Jouhten P., Rousu J. Inferring branching pathways in genome-scale metabolic networks. BMC Systems Biology 2009, 3:103.
71. Pitkänen E., Rantanen A., Rousu J., Ukkonen E. Finding feasible pathways in metabolic networks. Proceedings of the 10th Panhellenic Conference on Informatics (PCI'2005), Lecture Notes in Computer Science 2005, 123-133.
72. Planes F., Beasley J. A critical examination of stoichiometric and path-finding approaches to metabolic pathways. Briefings in Bioinformatics 2008, 9:422-436.
73. Rahman S., Advani P., Schunk R., Schrader R., Schomburg D. Metabolic pathway analysis web service (pathway hunter tool at cubic). Bioinformatics 2004, 21:1189-1193.
74. Schilling C., Letscher D., Palsson B. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. Journal of theoretical Biology 2000, 203:229-248.
75. Schuster S., Dandekar T., Fell D. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. TIBTECH 1999, 17:53-60.
76. Schuster S., de Figueiredo L.F., Kaleta C. Predicting novel pathways in genome-scale metabolic networks. Biochemical Society Transactions 2010, 38:1202-1205.
77. Scott M., Perkins T., Bunnell S., Pepin F., Thomas D., Hallett M. Identifying regulatory subnetworks for a set of genes. Molecular and Cellular Proteomics 2005, 4(5):683-692.
78. Shlomi T., Cabili M., Herrgard M., Palsson B., Ruppin E. Network-based prediction of human tissue-specic metabolism. Nature Biotechnology 2008, 26:1003-1010.
79. Sirava M., Schaefer T., Eiglsperger M., Kaufmann M., Kohlbacher O., Bornberg-Bauer E., Lenhof H. BioMiner-modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics 2002, 18(2):S219-S230.
80. Subramanian A., Tamayoa P., Mootha V., Mukherjeed S., Ebert B., Gillette M., Paulovich A., Pomeroy S., Golub T., Lander E., Mesirov J. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15545-15550.
81. Thiele I., Palsson B. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nature Protocol 2010, 5:93-121.
82. van Helden J., Gilbert D., Wernisch L., Schroeder M., Wodak S. Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data. Lecture Notes in Computer Science 2001, 2066:147-165.
83. van Helden J., Naim A., Mancuso R., Eldridge M., Wernisch L., Gilbert D., Wodak S. Representing and analysing molecular and cellular function in the computer. Biological Chemistry 2000, 381:921-935.
84. van Helden J., Wernisch L., Gilbert D., Wodak S. Graph-based analysis of metabolic networks. Ernst Schering Research Foundation Workshop, vol. 38 2002, 245-274.
85. Voss K., Heiner M., Koch I. Steady state analysis of metabolic pathways using Petri nets. In Silico Biology 2003, 3:367-387.
86. Wagner A., Fell D. The small world inside large metabolic networks. Proceedings of the Royal Society of London Series B 2001, 268:1803-1810.
87. Watts D., Strogatz S. Collective dynamics of 'small-world' networks. Nature 1998, 393:440-442.
88. Yen J. Finding the K shortest loopless paths in a network. Management Science 1971, 17:712-716.
89. Zien A., Küffner R., Zimmer R., Lengauer T. Analysis of gene expression data with pathway scores. Proceedings of the International Conference of Intelligent Systems Molecular Biology 2000, 407-417.
90. Zur H., Ruppin E., Shlomi T. iMAT: an integrative metabolic analysis tool. Bioinformatics 2010, 26:3140-3142.