Identifying neighborhoods of coordinated gene expression and metabolite profiles

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  Hancock, Timothy ^a   Wicker, Nicolas ^b   Takigawa, Ichigaku ^a   Mamitsuka, Hiroshi ^a  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACEGLUTAMIDE; ALANINE; ARGININE; ASPARAGINE; ASPARTIC ACID; CYSTEINE; GLUCOSE 6 PHOSPHATE; GLUTAMIC ACID; GLYCEROL; GLYCEROPHOSPHATE; GLYCINE; LACTOSE; MALIC ACID; METHIONINE; ORNITHINE; PUTRESCINE; PYRUVIC ACID; RIBOSE; SERINE; SUCCINIC ACID; THREONINE; TREHALOSE; TYROSINE; VALINE; XYLOSE; ESCHERICHIA COLI PROTEIN;

ARTICLE; COLD STRESS; COMPUTER PROGRAM; CORRELATION ANALYSIS; DATA MINING; GENE EXPRESSION; GENETIC TRANSCRIPTION; HEAT STRESS; MATHEMATICAL ANALYSIS; METABOLISM; METABOLITE; OXIDATIVE STRESS; BIOLOGY; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLOME; TEMPERATURE;

COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; METABOLIC NETWORKS AND PATHWAYS; METABOLOME; OXIDATIVE STRESS; TEMPERATURE;

EID: 84857091080     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0031345     Document Type: Article

References (43)

1. Gygi SP, Rochon Y, Franza BR, Aebersold R, (1999) Correlation between protein and mrna abundance in yeast. Mol Cell Biol 19: 1720-30.
2. Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, et al. (2003) Global analysis of protein expression in yeast. Nature 425: 737-41.
3. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, et al. (2007) Multiple high-throughput analyses monitor the response of e. coli to perturbations. Science 316: 593-7.
4. Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, et al. (2010) Metabolomic and transcriptomic stress response of escherichia coli. Mol Syst Biol 6: 364.
5. Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor MI, et al. (2006) Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol 142: 1380-96.
6. Gibon Y, Usadel B, Blaesing OE, Kamlage B, Hoehne M, et al. (2006) Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in arabidopsis rosettes. Genome Biol 7: R76.
7. Fendt SM, Buescher JM, Rudroff F, Picotti P, Zamboni N, et al. (2010) Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity. Mol Syst Biol 6: 356.
8. Cakir T, Patil KR, iIsen Onsan Z, Ulgen KO, Kirdar B, et al. (2006) Integration of metabolome data with metabolic networks reveals reporter reactions. Mol Syst Biol 2: 50.
9. Bradley PH, Brauer MJ, Rabinowitz JD, Troyanskaya OG, (2009) Coordinated concentration changes of transcripts and metabolites in saccharomyces cerevisiae. PLoS Comput Biol 5: e1000270.
10. Ihmels J, Levy R, Barkai N, (2004) Principles of transcriptional control in the metabolic network of saccharomyces cerevisiae. Nat Biotechnol 22: 86-92.
11. Takigawa I, Mamitsuka H, (2008) Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis. Bioinformatics 24: 250-257.
12. Kupiec M, Sharan R, Ruppin E, (2007) Genetic interactions in yeast: is robustness going bust? Mol Syst Biol 3: 97.
13. Kim PJ, Lee DY, Kim TY, Lee KH, Jeong H, et al. (2007) Metabolite essentiality elucidates robustness of escherichia coli metabolism. Proc Natl Acad Sci U S A 104: 13638-42.
14. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL, (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
15. Smart AG, Amaral LAN, Ottino JM, (2008) Cascading failure and robustness in metabolic networks. Proc Natl Acad Sci U S A 105: 13223-8.
16. Spirin V, Gelfand MS, Mironov AA, Mirny LA, (2006) A metabolic network in the evolutionary context: multiscale structure and modularity. Proc Natl Acad Sci U S A 103: 8774-9.
17. Holme P, (2011) Metabolic robustness and network modularity: a model study. PLoS One 6: e16605.
18. Handorf T, Ebenhoh O, Heinrich R, (2005) Expanding metabolic networks: scopes of compounds, robustness, and evolution. J Mol Evol 61: 498-512.
19. Hancock T, Takigawa I, Mamitsuka H, (2010) Mining metabolic pathways through gene expression. Bioinformatics 26: 2128-2135.
20. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E, (1953) Equations of state calculations by fast computing machines. Journal of Chemical Physics 21 or 6: 1087-1091.
21. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 102: 15545-15550.
22. Kanehisa M, Goto S, (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28: 27-30.
23. Metzner M, Germer J, Hengge R, (2004) Multiple stress signal integration in the regulation of the complex sigma s-dependent csid-ygaf-gabdtp operon in escherichia coli. Mol Microbiol 51: 799-811.
24. Hahn J, Hu Z, Thiele D, Iyer V, (2004) Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Molecular and cellular biology 24: 5249-5256.
25. Fischer D, Teich A, Neubauer P, Hengge-Aronis R, (1998) The general stress sigma factor sigmas of escherichia coli is induced during diauxic shift from glucose to lactose. J Bacteriol 180: 6203-6.
26. Krin E, Danchin A, Soutourina O, (2010) Rcsb plays a central role in h-ns-dependent regulation of motility and acid stress resistance in escherichia coli. Res Microbiol 161: 363-71.
27. Krin E, Danchin A, Soutourina O, (2010) Decrypting the h-ns-dependent regulatory cascade of acid stress resistance in escherichia coli. BMC Microbiol 10: 273.
28. Mandelstam J, (1957) Turnover of protein in starved bacteria and its relationship to the induced synthesis of enzyme. Nature 179: 1179-81.
29. Willetts NS, (1967) Intracellular protein breakdown in non-growing cells of escherichia coli. Biochem J 103: 453-61.
30. Patzer SI, Hantke K, (1998) The znuabc high-affinity zinc uptake system and its regulator zur in escherichia coli. Mol Microbiol 28: 1199-210.
31. Hantke K, (2001) Iron and metal regulation in bacteria. Curr Opin Microbiol 4: 172-7.
32. Koch D, Nies DH, Grass G, (2007) The rcnra (yohlm) system of escherichia coli: a connection between nickel, cobalt and iron homeostasis. Biometals 20: 759-71.
33. Munson GP, Lam DL, Outten FW, O'Halloran TV, (2000) Identification of a copper-responsive two-component system on the chromosome of escherichia coli k-12. J Bacteriol 182: 5864-71.
34. van Vliet AHM, Ketley JM, Park SF, Penn CW, (2002) The role of iron in campylobacter gene regulation, metabolism and oxidative stress defense. FEMS Microbiol Rev 26: 173-86.
35. Akana J, Fedorov AA, Fedorov E, Novak WRP, Babbitt PC, et al. (2006) D-ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily. Biochemistry 45: 2493-503.
36. Sobota JM, Imlay JA, (2011) Iron enzyme ribulose-5-phosphate 3-epimerase in escherichia coli is rapidly damaged by hydrogen peroxide but can be protected by manganese. Proc Natl Acad Sci U S A 108: 5402-7.
37. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, et al. (2007) A genome-scale metabolic reconstruction for escherichia coli k-12 mg1655 that accounts for 1260 orfs and thermodynamic information. Mol Syst Biol 3: 121.
38. Schellenberger J, Park JO, Conrad TM, Palsson BØ, (2010) Bigg: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11: 213.
39. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, et al. (2009) Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37: D619-22.
40. Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, et al. (2007) Reactome: a knowledge base of biologic pathways and processes. Genome Biol 8: R39.
41. Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-10.
42. Vazirani V, (2001) Approximation algorithms New York, NY, USA Springer Verlag.
43. IBM (2008) Ilog cplex optimizer version 11.1.0. http://www-01ibmcom/software/integration/optimization/cplex-optimizer/.