Topology of plant metabolic networks

Plant Metabolic Networks

Volumn , Issue , 2009, Pages 173-209

  Grafahrend Belau, Eva ^a   Junker, Björn H ^a   Klukas, Christian ^a   Koschützki, Dirk ^a   Schreiber, Falk ^a   Schwöbbermeyer, Henning ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84884064238     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-78745-9_7     Document Type: Chapter

References (122)

1. Albert I, Albert R (2004) Conserved network motifs allow protein-protein interaction prediction. Bioinformatics 20:3346-3352.
2. Arita M (2004) The metabolic world of Escherichia coli is not small. Proc Natl Acad Sci USA 101:1543-1547.
3. Artzy-Randrup Y, Fleishman SJ, Ben-Tal N, Stone L (2004) Comment on "Network motifs: Simple building blocks of complex networks" and "Superfamilies of evolved and designed networks". Science 305:1107c.
4. Backhaus K, Erichson B, Plinke W, Weiber R (2003) Multivariate Analysis Methods. An Application-Oriented Introduction, 10th ed., Springer, Berlin.
5. Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5:101-113.
6. Batagelj V, Mrvar A (2004) Pajek - Analysis and visualization of large networks. In: Jünger M, Mutzel P (eds) Graph Drawing Software (Mathematics and Visualization). Springer, Berlin/Heidelberg, pp. 77-103.
7. Becker MY, Rojas I (2001) A graph layout algorithm for drawing metabolic pathways. Bioinformatics 17:461-467.
8. Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry. W H Freeman, New York.
9. Borisjuk L, Hajirezaei MR, Klukas C, Rolletschek H, Schreiber F (2005) Integrating data from biological experiments into metabolic networks with the DBE information system. In Silico Biology 5:93-102.
10. Brandenburg FJ, Forster M, Pick A, Raitner M, Schreiber F (2004) BioPath - exploration and visualization of biochemical pathways. In: Jünger M, Mutzel P (eds) Graph Drawing Software (Mathematics and Visualization). Springer, Berlin/Heidelberg, pp. 215-236.
11. Brandenburg FJ, Jünger M, Mutzel P (1997) Algorithmen zum automatischen Zeichnen von Graphen. Informatik Spektrum 20:199-207.
12. Brandes U, Wagner D (2004) Visone - Analysis and visualization of social networks. In: Jünger M, Mutzel P (eds) Graph Drawing Software (Mathematics and Visualization). Springer, Berlin/Heidelberg, pp. 321-340.
13. Breitkreutz BJ, Stark C, Tyers M (2003) Osprey: A network visualization system. Genome Biology 4: R22.
14. Card SK, Mackinlay JD, Shneiderman B (1999) Readings in Information Visualization: Using Vision to Think. Morgan Kaufmann Publ. Inc., San Francisco, CA.
15. CellNetAnalyzer http://www.mpi-magdeburg.mpg.de/projects/cna/cna.html.
16. Chung HJ, Kim M, Park CH, Kim J, Kim JH (2004) ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using scalable vector graphics. Nucleic Acids Res 32(Web-Server-Issue):460-464.
17. Colantuoni C, Henry G, Zeger S, Pevsner J (2002) SNOMAD (standardization and normalization of microarray data): Web- Accessible gene expression data analysis. Bioinformatics 18:1540-1541.
18. Demir E, Babur, O Dogrusoz U, Gursoy A, Nisanci G, Cetin- Atalay R, Ozturk M (2002) PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 18:996-1003.
19. Di Battista G, Eades P, Tamassia R, Tollis IG (1994) Annotated bibliography on graph drawing algorithms. Comput Geom-Theor Appl 4:235-282.
20. Di Battista G, Eades P, Tammasia R, Tollis IG (1999) Graph drawing: Algorithms for the visualization of graphs. Prentice Hall, New Jersey.
21. Dobrin R, Beg QK, Barabási AL, Oltvai ZN (2004) Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics 5:10.
22. Dogrusoz U, Giral E, Cetintas A, Civril A, Demir E (2004) A compound graph layout algorithm for biological pathways. In: Pach J (ed.) Graph Drawing. Springer, Berlin/Heidelberg, pp. 442-447.
23. van Dongen SM (2000) Graph Clustering by Flow Simulation. Center for Mathematics and Computer Science, Amsterdam.
24. Dysvik B, Jonassen I (2001) J-Express: exploring gene expression data using Java. Bioinformatics 17:369-370.
25. Eades P (1984) A heuristic for graph drawing. Congr Numer 41:149-160.
26. Eades P, Sugiyama K (1990) How to draw a directed graph. J Inform Proc 13:424-437.
27. Ederer M, Sauter T, Bullinger E, Gilles ED, Allgöwer F (2003) An approach for dividing models of biological reaction networks into functional units. Simulation 79:703-716.
28. Eom YH, Lee S, Jeong H (2006) Exploring local structural organization of metabolic networks using subgraph patterns. J Theor Biol 241:823-829.
29. Everitt BS, Landau S, Leese M (2001) Cluster analysis. Oxford University Press Inc., New York.
30. FANMOD http://www.minet.uni-jena.de/∼wernicke/motifs/index.html.
31. Fellenberg M, Mewes HW (1999) Interpreting clusters of gene expression profiles in terms of metabolic pathways. In: Giegerich R, Hofestadt R, Lengauer T, Mewes W, Schomburg D, Vingron M, Wingender E (eds) German Conference on Bioinformatics, Springer. pp. 185-187.
32. Fiehn O, Kopka J, Dörmann P, Altmann T, Trethewey R, Willmitzer L (2000) Metabolite profiling for plant functional genomics. Nature Biotechnol 18:1157-1161.
33. Flux Coupling Finder, http://fenske.che.psu.edu/Faculty/CMaranas/programs.html.
34. Fruchterman TMJ, Reingold EM (1991) Graph drawing by force-directed placement. Software Practice and Experience 21:1129-1164.
35. Gagneur J, Jackson DB, Casari G (2003) Hierarchical analysis of dependency in metabolic networks. Bioinformatics 19:1027-1034.
36. Girvan M, Newman MEJ (2002) Community structure in social and biological networks. Proc Natl Acad Sci USA 99:7821-7826.
37. Girvan M, Newman MEJ (2004) Finding and evaluating community structure in networks. Phys Rev E 69(026113).
38. Guimera R, Nunes Amaral LA (2005) Functional cartography of complex metabolic networks. Nature 443:895-900.
39. Han J, Kamber M (2001) Data Mining, Concepts and Techniques. Morgan Kaufmann Publishers, USA.
40. HI www.tp.umu.se/forskning/networks/meta/.
41. Holme P, Huss M, Jeong H (2003) Subnetwork hierarchies of biochemical pathways. Bioinformatics 19:532-538.
42. Hood L, Perlmutter RM (2004) The impact of systems approaches on biological problems in drug discovery. Nature Biotechnol 22:1215-1217.
43. Hu Z, Mellor J, Wu J, Yamada T, Holloway D, DeLisi C (2005) VisANT: data-integrating visual framework for biological networks and modules. Nucl Acids Res 33(Web Server issue):W352-W3577.
44. Hu Z, Mellor JC, Wu J, DeLisi C (2004) VisANT: An online visualization and analysis tool for biological interaction data. BMC Bioinformatics 5:17.
45. Ingram PJ, Stumpf MP, Stark J (2006) Network motifs: Structure does not determine function. BMC Genomics 7:108.
46. Ishihara S, Fujimoto K, Shibata T (2005) Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes. Genes to Cells 10:1025-1038.
47. Jain AK, Dubes RC (1988) Algorithms for Clustering Data. Prentice Hall, New York.
48. Jain AK, Murty MN, Flynn PJ (1999) Data clustering: A review. ACM Computing Surveys 31:264-323.
49. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL (2000) The large-scale organization of metabolic networks. Nature 407:651-654.
50. Junker BH, Klukas C, Schreiber F (2006) VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7:109.
51. Junker BH, Koschützki D, Schreiber F (2006) Exploration of biological network centralities with CentiBiN. BMC Bioinformatics 7:219.
52. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354-D358.
53. Karp PD, Ouzounis CA, Moore-Kochlacs C (2005) Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research 33:6083-6089.
54. Karp PD, Paley S (1994) Automated drawing of metabolic pathways. In: Hunter L, Searls D, Shavlik J (eds) Proc. 3rd International Conference on Bioinformatics and Genome Research, AAAI Press, New Jersey, pp. 207-215.
55. Karp PD, Paley SM (1993) Representation of metabolic knowledge: Pathways. In: Altman R, Brutlag D, Karp PD, Lathrop R, Searls D (eds) Proc. 2nd International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, California, pp. 225-238.
56. Karp PD, Riley M, Paley SM, Pellegrini-Toole A, Krummenacker M (1999) EcoCyc: encyclopedia of Escherichia coli genes and metabolism. Nucleic Acids Res 27:55-58.
57. Karp PD, Riley M, Paley SM, Pellegrini-Toole A, Krummenacker M (2000) The EcoCyc and MetaCyc databases. Nucleic Acids Res 28:56-59.
58. Kashtan N, Itzkovitz S, Milo R, Alon U (2002) Mfinder Tool Guide. Tech. Rep. Department of Molecular Cell Biology and Computer Science & Applied Mathematics, Weizman Institute of Science, Rehovot, Israel.
59. Kashtan N, Itzkovitz S, Milo R, Alon U (2004) Topological generalizations of network motifs. Physical Review E 70:031909.
60. Kitano H (2004) Biological robustness. Nat Rev Genet 5:826-837.
61. Kitano H, Funahashi A, Matsuoka Y, Oda K (2005) Using process diagrams for the graphical representation of biological networks. Nature Biotechnol 23:961-966.
62. Koch I, Junker BH, Heiner M (2005) Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21: 1219-1226.
63. Koschützki D, Lehmann KA, Peeters L, Richter S, Tenfelde-Podehl D, Zlotowski O (2005) Centrality indices. In: Brandes U, Erlebach T (eds) Network Analysis: Methodological Foundations. Vol. 3418 of Lecture Notes in Computer Science (LNCS) Tutorial. Springer- Verlag, Springer Berlin/Heidelberg, pp. 16-61.
64. Kose F, Weckwerth W, Linke T, Fiehn, O (2001) Visualizing plant metabolomic correlation networks using clique-metabolite matrices. Bioinformatics 17:1198-1208.
65. Krause AE, Frank KA, Mason DM, Ulanowicz RE, Taylor WW (2003) Compartments revealed in food-web structure. Nature 426:282-285.
66. Krieger CJ, Zhang P, Müller LA, Wang A, Paley S, Arnaud M, Pick J, Rhee SY, Karp PD (2004) MetaCyc: A multiorganism data-base of metabolic pathways and enzymes. Nucleic Acids Res 32:438-442.
67. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Giord DK, Young RA (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
68. Lemke N, Heŕedia F, Barcellos CK, dos Reis AN, Mombach JCM (2004) Essentiality and damage in metabolic networks. Bioinformatics 20(1): 115-119.
69. Ma HW, Zeng AP (2003) The connectivity structure, giant strong component and centrality of metabolic networks. Bioinformatics 19: 1423-1430.
70. Ma HW, Zeng AP (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19:270-277.
71. Ma HW, Zhao XM, Yuan YJ, Zeng AP (2004) Decomposition of metabolic network into functional modules based on the global connectivity structure of reaction graph. Bioinformatics 20:1870-1876.
72. Mangan S, Itzkovitz S, Zaslaver A, Alon U (2006) The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J Mol Biol 356: 1073-1081.
73. Mangan S, Zaslaver A, Alon U (2003) The coherent feed-forward loop serves as a signsensitive delay element in transcription networks. J Mol Biol 334:197-204.
74. MAVisto http://mavisto.ipk-gatersleben.de/index.html.
75. Mfinder http://www.weizmann.ac.il/mcb/UriAlon/index.html.
76. Michal G (1999) Biochemical Pathways. Spektrum Akademischer Verlag, Heidelberg.
77. Middendorf M, Ziv E, Wiggins CH (2005) Inferring network mechanisms: The Drosophila melanogaster protein interaction network. Proc Natl Acad Sci USA 102:3192-3197.
78. Milo R, Itzkovitz S, Kashtan N, Levitt R, Shen-Orr S, Ayzenshtat I, Sheer M, Alon U (2004) Superfamilies of evolved and designed networks. Science 303:1538-1542.
79. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U (2002) Network motifs: Simple building blocks of complex networks. Science 298:824-827.
80. Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z (2005) PathwayExplorer: Web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Research 33:W633-W637.
81. Moreno JL (1934) Who Shall Survive?: A New Approach to the Problem of Human Interrelations. Nervous and Mental Disease Publishing Company, Washington.
82. Müller LA, Zhang P, Rhee SY (2003) AraCyc: A biochemical pathway database for Arabidopsis. Plant Physiol 132:453-460.
83. Nakao M, Bono H, Kawashima S, Kamiya T, Sato K, Goto S, Kanehisa M (1999) Genomescale gene expression analysis and pathway reconstruction in KEGG. Genome Informatics 10:94-103.
84. Nicholson, DE (1997) Metabolic Pathways Map (Poster). Sigma Chemical Co., St. Louis, St. Louis, MO.
85. Oltvai ZN, Barabási AL (2002) Systems biology: life's complexity pyramid. Science 298:763-764.
86. Pan D, Sun N, Cheung KH, Guan Z, Ma L, Holford M, Deng X, Zhao H (2003) PathMAPA: A tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. BMC Bioinformatics 4:56.
87. Papin JA, Reed JL, Palsson BO (2004) Hierarchical thinking in network biology: The unbiased modularization of biochemical networks. Trends Biochem Sci 29: 641-647.
88. Přzulj N, Corneil DG, Jurisica I (2004) Modeling interactome: Scale-free or geometric? Bioinformatics 20:3508-3515.
89. Quinn NR, Breuer MA (1979) A force directed component placement procedure for printed circuit boards. IEEE Trans Circuits Syst CAS 26:377-388.
90. Rahman SA, Schomburg D (2006) Observing local and global properties of metabolic pathways: "load points" and "choke points" in the metabolic networks. Bioinformatics 22: 1767-1774.
91. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555.
92. Rives AW, Galitski T (2003) Modular organization of cellular networks. Proc Natl Acad Sci USA 100:1128-1133.
93. Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie A (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13:11-29.
94. Rolletschek H, Radchuk S, Klukas C, Schreiber F, Borisjuk L (2005) Regulation of lipid biosynthesis in soybean seeds: evidence for a key role of photosynthetic oxygen release. New Phytologist 167:777-786.
95. Rost U, Kummer U (2004) Visualisation of biochemical network simulations with SimWiz. In: Iyengar R, Wolkenhauer O, Kolch W, Kwang-hyun Cho, Klingmuller U (eds) Systems Biology, IEE Proc. Vol. 1, pp. 184-189.
96. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Research, Database issue 32:D431-D433.
97. Schreiber F (2002) High quality visualization of biochemical pathways in BioPath. In Silico Biol 2:59-73.
98. Schreiber F, Schwöbbermeyer H (2005) MAVisto: A tool for the exploration of network motifs. Bioinformatics 21:3572-3574.
99. Schuster S, Pfeifer T, Moldenhauer F, Koch I, Dandekar T (2002) Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18:351-361.
100. SEPARATOR http://pinguin.biologie.uni-jena.de/bioinformatik/networks/separator/separator.html.
101. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504.
102. Shen-Orr S, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genetics 31:64-68.
103. Snel B, Bork P, Huynen MA (2002) The identification of functional modules from the genomic association of genes. Proc Natl Acad Sci USA 99:5890-5895.
104. Sokal RR, Michener CD (1958) A statistical method for evaluating systematic relationships. Univ Kansas Sci Bull 38:1409-1438.
105. Spirin V, Mirny LA (2003) Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci USA 100:12123-12128.
106. Sturn A, Quackenbush J, Trajanoski Z (2002) Genesis: Cluster analysis of microarray data. Bioinformatics 18:207-208.
107. Sugiyama K, Tagawa S, Toda M (1981) Methods for visual understanding of hierarchical systems. IEEE Trans Syst Man Cybern 11:109-125.
108. Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) MAPMAN: A user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37: 914-939.
109. Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibatanenell D (2005) KaPPA-View. A web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol 138: 1289-1300.
110. Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S, Stitt M (2005) Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiol 138:1195-1204.
111. Wagner A, Fell DA (2001) The small world inside large metabolic networks. Proc Royal Society London B 268:1803-1810.
112. Wall ME, Dunlop MJ, Hlavacek WS (2005) Multiple functions of a feed-forward-loop gene circuit. J Mol Biol 349:501-514.
113. Wegner K, Kummer U (2005) A new dynamical layout algorithm for complex biochemical reaction networks. BMC Bioinformatics 6:212.
114. Wernicke S, Rasche F (2006) FANMOD: A tool for fast network motif detection. Bioinformatics 22:1152-1153.
115. Wiese R, Eiglsperger M, Kaufmann M (2001) Visualization and automatic layout of graphs. In: Mutzel P, Jünger M, Leipert S (eds) Proc. 9th International Symposium on Graph Drawing (GD 2001). Springer, Berlin/Heidelberg, pp. 453-462.
116. Wolf G (2000) Visualising gene expression in its metabolic context. Briefings in Bioinformatics 1:297-304.
117. Wuchty S, Oltvai ZN, Barabási AL (2003) Evolutionary conservation of motif constituents in the yeast protein interaction network. Nature Genet 35:176-179.
118. Wuchty S, Stadler PF (2003) Centers of complex networks. J Theor Biol 223: 45-53.
119. Zamora Lopez G, Steuer R (2008) Global network properties. In: BH Junker, Schreiber F (eds.) Analysis of Biological Networks. John Wiley & Sons, Hoboken, NJ, pp. 31-63.
120. Zhang LV, King OD, Wong SL, Goldberg DS, Tong AHY, Lesage G, Andrews B, Bussey H, Boone C, Rot FP (2005) Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. J Biol 4:6.
121. Zhao J, Yu H, Luo JH, Cao ZW, Li YX (2006) Hierarchical modularity of nested bow-ties in metabolic networks. BMC Bioinformatics 7:386.
122. Zhu D, Qin ZS (2005) Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics 6: 851.