Dynamics of time-lagged gene-to-metabolite networks of Escherichia coli elucidated by integrative omics approach

OMICS A Journal of Integrative Biology

Volumn 15, Issue 1-2, 2011, Pages 15-23

  Takahashi, Hiroki ^a   Morioka, Ryoko ^b   Ito, Ryosuke ^a   Oshima, Taku ^a   Altaf Ul Amin, Md ^a   Ogasawara, Naotake ^a   Kanaya, Shigehiko ^a  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b Japan Biological Information Research Center   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; PHOSPHOLIPID;

ARTICLE; BIOSYNTHESIS; DNA MICROARRAY; ESCHERICHIA COLI; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; METABOLOMICS; NONHUMAN; PRIORITY JOURNAL; TRANSCRIPTOMICS;

ESCHERICHIA COLI; FOURIER ANALYSIS; GENE EXPRESSION PROFILING; MASS SPECTROMETRY; METABOLOMICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SPECTROSCOPY, FOURIER TRANSFORM INFRARED;

ESCHERICHIA COLI;

EID: 79551567038     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2010.0074     Document Type: Article

References (27)

1. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-29.
2. Balasubramaniyan, R., Hullermeier, E., Weskamp, N., and Kamper, J. (2005). Clustering of gene expression data using a local shape-based similarity measure. Bioinformatics 21, 1069-1077.
3. Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57, 289-300.
4. Castrillo, J.I., and Oliver, S.G. (2004). Yeast as a touchstone in post-genomic research: strategies for integrative analysis in functional genomics. J Biochem Mol Biol 31, 93-106.
5. Daran-Lapujade, P., Rossell, S., Gulik, W., Luttik, M., Groot, M., Slijper, M., et al. (2007). The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc Natl Acad Sci USA 104, 15753-15758.
6. Dudoit, S., Fridlyand, J., and Speed, T. (2002). Comparison of discrimination methods for the classification of tumors using gene expression data. J Am Stat Assoc 97, 77-87.
7. Fiehn, O., Kloska, S., and Altmann, T. (2001). Integrated studies on plant biology using multiparallel techniques. Curr Opin Biotechnol 12, 82-86.
8. Fridman, E., and Pichersky, E. (2005). Metabolomics, genomics, proteomics, and the identification of enzymes and their substrates and products. Curr Opin Plant Biol 8, 242-248.
9. Grogan, D., and Cronan, J. (1997). Cyclopropane ring formation in membrane lipids of bacteria. Microbiol Mol Biol Rev 61, 429-441.
10. Hirai, M.Y., Yano, M., Goodenowe, D.B., Kanaya, S., Kimura, T., Awazuhara, M., et al. (2004). Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci USA 101, 10205-10210.
11. Hirai, M.Y., Klein, M., Fujikawa, Y., Yano, M., Goodenowe, D.B., Yamazaki, Y., et al. (2005). Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem 280, 25590-25595.
12. Ji, L., and Tan, K.L. (2005). Identifying time-lagged gene clusters using gene expression data. Bioinformatics 21, 509-516.
13. Kalman, R.E., and Bucy, R.S. (1961). New results in linear filtering and prediction theory. Trans ASME J Basic Eng 83, 95-107.
14. Keseler, I.M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I.T., et al. (2005). EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 33, D334-D337.
15. Kobayashi, H., Akitomi, J., Fujii, N., Kobayashi, K., Altaf-UL-Amin, M., Kurokawa, K., et al. (2007) The entire organization of transcription units on the Bacillus subtilis genome. BMCGenomics 8, 197.
16. Morioka, R., Kanaya, S., Hirai, M.Y., Yano, M., Ogasawara, N., and Saito, K. (2007). Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model. BMC Bioinformatics 8, 343.
17. Pir, P., Kirdar, B., Hayes, A., Onsan, Z.Y., Ulgen, K.O., and Oliver, S.G. (2006). Integrative investigation of metabolic and transcriptomic data. BMC Bioinformatics 12, 203.
18. Quackenbush, J. (2002). Microarray data normalization and transformation. Nat Genet 32, 496-501.
19. Ralser, M., Wamelink, M., Latkolik, S., Jansen, E., Lehrach, H., and Jakobs, C. (2009). Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response. Nat Biotechnol 27, 604-605.
20. Redestig, H., Weicht, D., Selbig, J., and Hannah, M. A. (2007). Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana. BMC Bioinformatics 8, 454.
21. Saha, S.K., Nishijima, S., Matsuzaki, H., Shibuya, I., and Matsumoto, K. (1996a). A regulatory mechanism for the balancedsynthesis of membrane phospholipid species in Escherichia coli. Biosci Biotechnol Biochem 60, 111-116.
22. Saha, S.K., Furukawa, Y., Matsuzaki, H., Shibuya, I., and Matsumoto, K. (1996b). Directed mutagenesis, Ser-56 to Pro, of Bacillus subtilis phosphatidylserine synthase drastically lowers enzymatic activity and relieves amplification toxicity in Escherichia coli. Biosci Biotechnol Biochem 60, 630-633.
23. Takahashi, H., Kai, K., Shinbo, Y., Tanaka, K., Ohta, D., Oshima, T., et al. (2008). Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry. Anal Bioanal Chem 391, 2769-2782.
24. Urbanczyk-Wochniak, E., Luedemann, A., Kopka, J., Selbig, J., Roessner-Tunali, U., Willmitzer, L., et al. (2003). Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep 4, 989-993.
25. Walther, D., Strassburg, K., Durek, P., and Kopka, J. (2010). Metabolic pathway relationships revealed by an integrative analysis of the transcriptional and metabolic temperature stress-response dynamics in yeast. Omics 14, 261-274.
26. Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J., et al. (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30, e15.
27. Zhang, Y.M., and Rock, C.O. (2008). Membrane lipid homeostasis in bacteria. Nat Rev Microbiol 6, 222-233.