A method for finding metabolic pathways using atomic group tracking

PLoS ONE

Volumn 12, Issue 1, 2017, Pages

  Huang, Yiran ^a,b   Zhong, Cheng ^b   Lin, Hai Xiang ^c   Wang, Jianyi ^b  

^a SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

^b GUANGXI UNIVERSITY   (China)

^c Department of Microelectronics   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EXPERIMENTAL MODEL; FEASIBILITY STUDY; METABOLITE; THERMODYNAMICS; ALGORITHM; BIOLOGY; CHEMICAL MODEL; COMPUTER SIMULATION; FACTUAL DATABASE; METABOLISM; PROCEDURES;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, FACTUAL; METABOLIC NETWORKS AND PATHWAYS; MODELS, CHEMICAL; THERMODYNAMICS;

EID: 85009103532     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0168725     Document Type: Article

References (56)

1. Blum T, Kohlbacher O. MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics. 2008; 24(18):2108-9. doi: 10.1093/bioinformatics/btn360 PMID: 18635573
2. Heath AP, Bennett GN, Kavraki LE. An algorithm for efficient identification of branched metabolic pathways. Journal of Computational Biology. 2011; 18(11):1575-97. doi: 10.1089/cmb.2011.0165 PMID: 21999288
3. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Research. 2014; 42(D1):D199-D205.
4. Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research. 2014; 42(D1):D459-D71.
5. Khosraviani M, Zamani MS, Bidkhori G. FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction. Bioinformatics. 2016; 32(3):398-408. doi: 10.1093/bioinformatics/btv578 PMID: 26454274
6. 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(6):565-76. doi: 10.1089/cmb.2008.0044 PMID: 18631021
7. Pey J, Prada J, Beasley JE, Planes FJ. Path finding methods accounting for stoichiometry in metabolic networks. Genome Biol. 2011; 12(5):R49. doi: 10.1186/gb-2011-12-5-r49 PMID: 21619601
8. Pey J, Valgepea K, Rubio A, Beasley JE, Planes FJ. Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. BMC Systems Biology. 2013; 7(1):134.
9. Pey J, Planes FJ, Beasley JE. Refining carbon flux paths using atomic trace data. Bioinformatics. 2014; 30(7):975-80. doi: 10.1093/bioinformatics/btt653 PMID: 24273244
10. Tervo CJ, Reed JL. MapMaker and PathTracer for tracking carbon in genome-scale metabolic models. Biotechnology Journal. 2016; 11(5):648-61. doi: 10.1002/biot.201500267 PMID: 26771089
11. Pharkya P, Burgard AP, Maranas CD. OptStrain: a computational framework for redesign of microbial production systems. Genome Research. 2004; 14(11):2367-76. doi: 10.1101/gr.2872004 PMID: 15520298
12. Chowdhury A, Maranas CD. Designing overall stoichiometric conversions and intervening metabolic reactions. Scientific Reports. 2015; 5(6 Pt 1):C1362.
13. Ismail MA, Deris S, Mohamad MS, Abdullah A. A newton cooperative genetic algorithm method for In Silico optimization of metabolic pathway production. PLoS ONE. 2015; 10(5):e0126199. doi: 10.1371/journal.pone.0126199 PMID: 25961295
14. Fehér T, Planson AG, Carbonell P, Fernández-Castané A, Grigoras I, Dariy E, et al. Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering. Biotechnology Journal. 2014; 9(11):1446-57. doi: 10.1002/biot.201400055 PMID: 25224453
15. Dale JM, Popescu L, Karp PD. Machine learning methods for metabolic pathway prediction. BMC Bioinformatics. 2010; 11(1):1.
16. Boudellioua I, Saidi R, Hoehndorf R, Martin MJ, Solovyev V. Prediction of metabolic pathway involvement in prokaryotic UniProtKB data by association rule mining. PLoS ONE. 2016; 11(7):e0158896. doi: 10.1371/journal.pone.0158896 PMID: 27390860
17. Gerard MF, Stegmayer G, Milone DH. An evolutionary approach for searching metabolic pathways. Computers in Biology and Medicine. 2013; 43(11):1704-12. doi: 10.1016/j.compbiomed.2013.08.017 PMID: 24209916
18. Gerard MF, Stegmayer G, Milone DH. EvoMS: An evolutionary tool to find de novo metabolic pathways. Biosystems. 2015; 134:43-7. doi: 10.1016/j.biosystems.2015.04.006 PMID: 26092635
19. McClymont K, Soyer OS. Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. Nucleic Acids Research. 2013; 41(11):e113-e. doi: 10.1093/nar/gkt234 PMID: 23580552
20. McShan DC, Rao S, Shah I. PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics. 2003; 19(13):1692-8. doi: 10.1093/bioinformatics/btg217 PMID: 12967966
21. Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metabolic Engineering. 2014; 25:140-58. doi: 10.1016/j.ymben.2014.07.009 PMID: 25080239
22. Cho A, Yun H, Park JH, Lee SY, Park S. Prediction of novel synthetic pathways for the production of desired chemicals. BMC Systems Biology. 2010; 4(1):1.
23. Carbonell P, Fichera D, Pandit SB, Faulon J-L. Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Systems Biology. 2012; 6(1):10.
24. Tabei Y, Yamanishi Y, Kotera M. Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction. Bioinformatics. 2016; 32(12):i278-i87. doi: 10.1093/bioinformatics/btw260 PMID: 27307627
25. Lim K, Wong L. CMPF: Class-switching minimized pathfinding in metabolic networks. BMC Bioinformatics. 2012; 13(Suppl 17):S17.
26. Faust K, Dupont P, Callut J, Van Helden J. Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics. 2010; 26(9):1211-8. doi: 10.1093/bioinformatics/btq105 PMID: 20228128
27. Planes FJ, Beasley JE. A critical examination of stoichiometric and path-finding approaches to metabolic pathways. Briefings in Bioinformatics. 2008; 9(5):422-36. doi: 10.1093/bib/bbn018 PMID: 18436574
28. De Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, et al. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics. 2009; 25(23):3158-65. doi: 10.1093/bioinformatics/btp564 PMID: 19793869
29. Fernández-Castané A, Fehér T, Carbonell P, Pauthenier C, Faulon J-L. Computer-aided design for metabolic engineering. Journal of Biotechnology. 2014; 192:302-13. doi: 10.1016/j.jbiotec.2014.03.029 PMID: 24704607
30. Pitkänen E, Jouhten P, Rousu J. Inferring branching pathways in genome-scale metabolic networks. BMC Systems Biology. 2009; 3(1):1.
31. Liu F, Vilaça P, Rocha I, Rocha M. Development and application of efficient pathway enumeration algorithms for metabolic engineering applications. Computer Methods and Programs in Biomedicine. 2015; 118(2):134-46. doi: 10.1016/j.cmpb.2014.11.010 PMID: 25580014
32. Arita M. In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. Genome Research. 2003; 13(11):2455-66. doi: 10.1101/gr.1212003 PMID: 14559781
33. 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(6):1543-7. doi: 10.1073/pnas.0306458101 PMID: 14757824
34. Ma H, Zeng A-P. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics. 2003; 19(2):270-7. PMID: 12538249
35. Gerlee P, Lizana L, Sneppen K. Pathway identification by network pruning in the metabolic network of Escherichia coli. Bioinformatics. 2009; 25(24):3282-8. doi: 10.1093/bioinformatics/btp575 PMID: 19808881
36. Ranganathan S, Maranas CD. Microbial 1-butanol production: Identification of non-native production routes and in silico engineering interventions. Biotechnology Journal. 2010; 5(7):716-25. doi: 10.1002/biot.201000171 PMID: 20665644
37. Croes D, Couche F, Wodak SJ, van Helden J. Inferring meaningful pathways in weighted metabolic networks. Journal of Molecular Biology. 2006; 356(1):222-36. doi: 10.1016/j.jmb.2005.09.079 PMID: 16337962
38. Xia D, Zheng H, Liu Z, Li G, Li J, Hong J, et al. MRSD: a web server for Metabolic Route Search and Design. Bioinformatics. 2011; 27(11):1581-2. doi: 10.1093/bioinformatics/btr160 PMID: 21450713
39. Yousofshahi M, Lee K, Hassoun S. Probabilistic pathway construction. Metabolic Engineering. 2011; 13 (4):435-44. doi: 10.1016/j.ymben.2011.01.006 PMID: 21292021
40. Pertusi DA, Stine AE, Broadbelt LJ, Tyo KE. Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics. 2015; 31(7):1016-24. doi: 10.1093/bioinformatics/btu760 PMID: 25417203
41. Rahman SA, Advani P, Schunk R, Schrader R, Schomburg D. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics. 2005; 21(7):1189-93. doi: 10.1093/bioinformatics/bti116 PMID: 15572476
42. Kotera M, Hattori M, Oh M-A, Yamamoto R, Komeno T, Yabuzaki J, et al. RPAIR: a reactant-pair database representing chemical changes in enzymatic reactions. Genome Informatics. 2004; 15:P062.
43. Boyer F, Viari A. Ab initio reconstruction of metabolic pathways. Bioinformatics. 2003; 19(suppl 2):ii26- ii34.
44. Faust K, Croes D, van Helden J. Metabolic pathfinding using RPAIR annotation. Journal of Molecular Biology. 2009; 388(2):390-414. doi: 10.1016/j.jmb.2009.03.006 PMID: 19281817
45. Zhou W, Nakhleh L. The strength of chemical linkage as a criterion for pruning metabolic graphs. Bioinformatics. 2011; 27(14):1957-63. doi: 10.1093/bioinformatics/btr271 PMID: 21551141
46. Heath AP, Bennett GN, Kavraki LE. Finding metabolic pathways using atom tracking. Bioinformatics. 2010; 26(12):1548-55. doi: 10.1093/bioinformatics/btq223 PMID: 20421197
47. Latendresse M, Krummenacker M, Karp PD. Optimal metabolic route search based on atom mappings. Bioinformatics. 2014; 30(14):2043-50. doi: 10.1093/bioinformatics/btu150 PMID: 24642060
48. Mithani A, Preston GM, Hein J. Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison. Bioinformatics. 2009; 25(14):1831-2. doi: 10.1093/bioinformatics/btp269 PMID: 19398450
49. Zhou W, Nakhleh L. Quantifying and assessing the effect of chemical symmetry in metabolic pathways. Journal of Chemical Information and Modeling. 2012; 52(10):2684-96. doi: 10.1021/ci300259u PMID: 22985501
50. Flamholz A, Noor E, Bar-Even A, Milo R. eQuilibrator-the biochemical thermodynamics calculator. Nucleic Acids Research. 2012; 40(D1):D770-D5.
51. Asad Rahman S, Bashton M, Holliday G, Schrader R, Thornton J. Small Molecule Subgraph Detector (SMSD) Toolkit. J. Cheminform. 2009; 1:12. doi: 10.1186/1758-2946-1-12 PMID: 20298518
52. Lemer C, Antezana E, Couche F, Fays F, Santolaria X, Janky RS, et al. The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Research. 2004; 32(suppl 1): D443-D8.
53. Markatou M, Tian H, Biswas S, Hripcsak GM. Analysis of variance of cross-validation estimators of the generalization error. Journal of Machine Learning Research. 2005; 6:1127-68.
54. Hripcsak G, Rothschild AS. Agreement, the f-measure, and reliability in information retrieval. Journal of the American Medical Informatics Association. 2005; 12(3):296-8. doi: 10.1197/jamia.M1733 PMID: 15684123
55. Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, et al. EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Research. 2009; 37(suppl 1): D464-D70.
56. Alcántara R, Axelsen KB, Morgat A, Belda E, Coudert E, Bridge A, et al. Rhea-a manually curated resource of biochemical reactions. Nucleic Acids Research. 2012; 40(D1):D754-D60.