Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

BMC Systems Biology

Volumn 4, Issue , 2010, Pages

  Radrich, Karin ^a,b   Tsuruoka, Yoshimasa ^a,c   Dobson, Paul ^a   Gevorgyan, Albert ^d,e   Swainston, Neil ^a   Baart, Gino ^f   Schwartz, Jean Marc ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^d OXFORD BROOKES UNIVERSITY   (United Kingdom)

^e UNIVERSITY OF SURREY   (United Kingdom)

^f GHENT UNIVERSITY   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS; ARTICLE; FACTUAL DATABASE; GENETICS; GENOME; GENOMICS; METABOLISM; METHODOLOGY; REPRODUCIBILITY;

ARABIDOPSIS; DATABASES, FACTUAL; GENOME; GENOMICS; METABOLIC NETWORKS AND PATHWAYS; REPRODUCIBILITY OF RESULTS;

EID: 77955534569     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-114     Document Type: Article

References (52)

1. Sweetlove LJ, Fell DA, Fernie AR. Getting to grips with the plant metabolic network. Biochem J 2008, 409:27-41. 10.1042/BJ20071115, 18062772.
2. Green ML, Karp PD. The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res 2006, 34:3687-97. 10.1093/nar/gkl438, 1540720, 16893953.
3. Heinemann M, Kümmel A, Ruinatscha R, Panke S. In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol Bioeng 2005, 92:850-64. 10.1002/bit.20663, 16155945.
4. Oh YK, Palsson B, Park SM, Schilling CH, Mahadevan R. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 2007, 282:28791-9. 10.1074/jbc.M703759200, 17573341.
5. Resendis-Antonio O, Reed JL, Encarnación S, Collado-Vides J, Palsson B. Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli. PLoS Comput Biol 2007, 3:1887-95. 10.1371/journal.pcbi.0030192, 2000972,2000972, 17922569.
6. Andersen MR, Nielsen ML, Nielsen J. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger. Mol Syst Biol 2008, 4:178. 10.1038/msb.2008.12, 2290933, 18364712.
7. Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Ki{dotless}rdar B, Penttilä M, Klipp E, Palsson B, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008, 26:1155-60. 10.1038/nbt1492, 18846089.
8. Sheikh K, Förster J, Nielsen LK. Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus. Biotechnol Prog 2005, 21:112-21. 10.1021/bp0498138, 15903248.
9. Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson B. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci USA 2007, 6:1777-82.
10. Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, Goryanin I. The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol 2007, 3:135. 10.1038/msb4100177, 2013923, 17882155.
11. Feist AM, Palsson B. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 2008, 26:659-67. 10.1038/nbt1401, 18536691.
12. Lee DS, Burd H, Liu J, Almaas E, Wiest O, Barabási AL, Oltvai ZN, Kapatral V. Comparative genome-scale metabolic reconstruction and flux balance analysis of multiple Staphylococcus aureus genomes identify novel anti-microbial drug targets. J Bacteriol 2009, 191:4015-24. 10.1128/JB.01743-08, 2698402, 19376871.
13. Suthers PF, Dasika MS, Kumar VS, Denisov G, Glass JI, Maranas CD. A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189. PLoS Comput Biol 2009, 5:e1000285. 10.1371/journal.pcbi.1000285, 2633051, 19214212.
14. Ginsburg H. Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium. Trends Parasitol 2009, 25:37-43. 10.1016/j.pt.2008.08.012, 18986839.
15. Poolman MG, Bonde BK, Gevorgyan A, Patel HH, Fell DA. Challenges to be faced in the reconstruction of metabolic networks from public databases. Syst Biol 2006, 153:379-84.
16. Poolman MG, Miguet L, Sweetlove LJ, Fell DA. A genome-scale metabolic model of Arabidopsis thaliana and some of its properties. Plant Physiol 2009, 151:1570-81. 10.1104/pp.109.141267, 19755544.
17. de Oliveira Dal'Molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK. AraGEM - A genome-scale reconstruction of the primary metabolic network in Arabidopsis thaliana. Plant Physiol 2010, 152:579-89. 10.1104/pp.109.148817, 20044452.
18. Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SY. MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol 2005, 138:27-37. 10.1104/pp.105.060376, 1104157, 15888675.
19. 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 Res 2008, 36:D480-4. 10.1093/nar/gkm882, 2238879, 18077471.
20. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcántara R, Darsow M, Guedj M, Ashburner M. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 2008, 36:D344-50. 10.1093/nar/gkm791, 2238832, 17932057.
21. Buntrock RE. Chemical registries - in the fourth decade of service. J Chem Inf Comput Sci 2001, 41:259-63.
22. Austin CP, Brady LS, Insel TR, Collins FS. NIH Molecular Libraries Initiative. Science 2004, 306:1138-39. 10.1126/science.1105511, 15542455.
23. Tsuruoka Y, McNaught J, Tsujii J, Ananiadou S. Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. Bioinformatics 2007, 23:2768-74. 10.1093/bioinformatics/btm393, 17698493.
24. Hassan M, Brown RD, Varma-O'Brien S, Rogers D. Cheminformatics analysis and learning in a data pipelining environment. Mol Divers 2006, 10:283-99. 10.1007/s11030-006-9041-5, 17031533.
25. Weininger D, Weininger A, Weininger JL. SMILES. 2. Algorithm for generation of unique SMILES notation. J Chem Inf Comput Sci 1989, 29:97-101.
26. Willett P. Similarity-based virtual screening using 2 D fingerprints. Drug Discov Today 2006, 11:1046-53. 10.1016/j.drudis.2006.10.005, 17129822.
27. Gevorgyan A, Poolman MG, Fell DA. Detection of stoichiometric inconsistencies in biomolecular models. Bioinformatics 2008, 24:2245-51. 10.1093/bioinformatics/btn425, 18697772.
28. Nikolaev EV, Burgard AP, Maranas CD. Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions. Biophys J 2005, 88:37-49. 10.1529/biophysj.104.043489, 1305013, 15489308.
29. Bornstein BJ, Keating SM, Jouraku A, Hucka M. LibSBML: an API library for SBML. Bioinformatics 2008, 24:880-1. 10.1093/bioinformatics/btn051, 2517632, 18252737.
30. Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 2005, 23:1509-15. 10.1038/nbt1156, 16333295.
31. Stein SE, Heller SR, Tchekhovskoi D. An open standard for chemical structure representation: The IUPAC chemical identifier. Proceedings of the 2003 International Chemical Information Conference (Nîmes), Infonortics 2003, 131-43.
32. Huala E, Dickerman A, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang J, Huang W, Mueller L, Bhattacharyya D, Bhaya D, Sobral B, Beavis B, Somerville C, Rhee SY. The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 2001, 29:102-5. 10.1093/nar/29.1.102, 29827, 11125061.
33. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-504. 10.1101/gr.1239303, 403769, 14597658.
34. Assenov Y, Ramírez F, Schelhorn SE, Lengauer T, Albrecht A. Computing topological parameters of biological networks. Bioinformatics 2008, 24:282-4. 10.1093/bioinformatics/btm554, 18006545.
35. Dong J, Horvath S. Understanding network concepts in modules. BMC Syst Biol 2007, 1:24. 10.1186/1752-0509-1-24, 17547772.
36. Reed JL, Vo TD, Schilling CH, Palsson B. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4:R54. 10.1186/gb-2003-4-9-r54, 193654, 12952533.
37. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL. The large-scale organization of metabolic networks. Nature 2000, 407:651-4. 10.1038/35036627, 11034217.
38. Wagner A, Fell DA. The small world inside large metabolic networks. Proc R Soc Lond B Biol Sci 2001, 268:1803-10.
39. Almaas E. Biological impacts and context of network theory. J Exp Biol 2007, 210:1548-58. 10.1242/jeb.003731, 17449819.
40. Ma H, Zeng AP. Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 2003, 19:270-7. 10.1093/bioinformatics/19.2.270, 12538249.
41. Arita M. The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci USA 2004, 101:1543-47. 10.1073/pnas.0306458101, 341771, 14757824.
42. Edwards JS, Palsson B. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 2000, 97:5528-33. 10.1073/pnas.97.10.5528, 25862, 10805808.
43. Förster J, Famili I, Fu P, Palsson B, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13:244-53. 10.1101/gr.234503, 420374, 12566402.
44. D'Auria JC, Gershenzon J. The secondary metabolism of Arabidopsis thaliana: growing like a weed. Curr Opin Plant Biol 2005, 8:308-16. 10.1016/j.pbi.2005.03.012, 15860428.
45. Clay NK, Adio AM, Denoux C, Jander G, Ausubel FM. Glucosinolate metabolites required for an Arabidopsis innate immune response. Science 2009, 323:95-101. 10.1126/science.1164627, 2630859, 19095898.
46. Bednarek P, Pislewska-Bednarek M, Svatos A, Schneider B, Doubsky J, Mansurova M, Humphry M, Consonni C, Panstruga R, Sanchez-Vallet A, Molina A, Schulze-Lefert P. A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense. Science 2009, 323:101-6. 10.1126/science.1163732, 19095900.
47. Dörmann P. Functional diversity of tocochromanols in plants. Planta 2007, 225:269-76. 10.1007/s00425-006-0438-2, 17115182.
48. Alcázar R, Marco F, Cuevas JC, Patron M, Ferrando A, Carrasco P, Tiburcio AF, Altabella T. Involvement of polyamines in plant response to abiotic stress. Biotechnol Lett 2006, 28:1867-76. 10.1007/s10529-006-9179-3, 17028780.
49. Woo HH, Jeong BR, Hawes MC. Flavonoids: from cell cycle regulation to biotechnology. Biotechnol Lett 2005, 27:365-74. 10.1007/s10529-005-1521-7, 15834800.
50. Mo ML, Palsson B. Understanding human metabolic physiology: a genome-to-systems approach. Trends Biotechnol 2009, 27:37-44. 10.1016/j.tibtech.2008.09.007, 19010556.
51. Thiele I, Palsson B. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protocols 2010, 5:93-121.
52. myExperiment. , http://www.myexperiment.org/packs/121