Skip to main content

MetNet: Systems Biology Tools for Arabidopsis

  • Conference paper

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Che, P., Weaver, L.M., Wurtele, E.S., and Nikolau, B.J., 2003, The role of biotin in regulating 3-methylcrotonyl-CoA carboxylase expression in Arabidopsis, Plant Physiol. 131:1479-1486.

    Article  CAS  PubMed  Google Scholar 

  • Che, P., Wurtele, E.S., and Nikolau, B.J., 2002, Metabolic and Environmental Regulation of 3-Methylcrotonyl-CoA Carboxylase Expression in Arabidopsis, Plant Physiol. 129:625-637.

    Article  CAS  PubMed  Google Scholar 

  • Cook, D., Hofmann, H., Lee, E-K., Yang, H., Nikolau, B., Wurtele, E.S., 2004, Visual Methods for Data from Two Factor Single Replicate Gene Expression Studies, Technical Report, Department of Statistics, Iowa State University 04-06: http://www.stat.iastate.edu/preprint/articles/2004-04.pdf.

  • Dickerson, J.A., Berleant, D.A., Du, P., Ding, J., Foster, C.M., Ling, L., and Wurtele, E.S., 2005, Creating modeling and visualizing metabolic networks, in: Medical Informatics, H. Chen, H., S.S. Fuller, S.S., C. Friedman, C., and W. Hirsch, W., eds., Springer Verlag, pp. 491-518.

    Google Scholar 

  • Ding, J., Berleant, D., Nettleton, D.E., and Wurtele, E.S., 2002, Mining medline: abstracts, sentences, or phrases? Pacific Symposium on Biocomputing, 1-12.

    Google Scholar 

  • Du, P., Gong, J., Wurtele, E.S., Dickerson, J.A., 2005, Modeling Gene Expression Networks using Fuzzy Logic, IEEE Trans. On Systems, Man and Cybernetics, Part B 35(6): 1351-1359.

    Article  Google Scholar 

  • Fernie, A.R., Geigenberger, P., and Stitt, M., 2005, Flux an important, but neglected compo-nent of functional genomics, Current Opinion in Plant Biology 8:174-182.

    Article  CAS  PubMed  Google Scholar 

  • Lange, B.M., and Ghassemian, M., 2005, Comprehensive post-genomic data analysis approaches integrating biochemical pathway map, Phytochemistry 66:413-451.

    Article  CAS  PubMed  Google Scholar 

  • Lee, E-K., Cook, D., Hofmann, H., Wurtele, E., Kim, D., Kim, J., and An, H., 2004, Gene-gobi: visual data analysis tools for microarray data compstat’ 2004 Symposium c Physica-Verlag/Springer.

    Google Scholar 

  • Lee, S.G., Kim, C.M., Hwang, K.S., 2005, Development of a software tool for in silico simu-lation of Escherichia coli using a visual programming environment, J. Biotechnol. (Epub).

    Google Scholar 

  • Ma’ayan, A., Blitzer, R.D., and Iyengar, R., 2005, Toward predictive models of mammalian cells, Annu. Rev. Biophys. Biomol. Struct. 34:319-349.

    Article  PubMed  Google Scholar 

  • Mueller, L.A., Zhang, P., and Rhee, S.Y., 2003, AraCyc: A Biochemical Pathway Database for Arabidopsis, Plant Physiology 132:453-460.

    Article  CAS  PubMed  Google Scholar 

  • Nikiforova, V.J., Daub, C.O., Hesse, H., Willmitzer, L., and Hoefgen, R., 2005. Integrative gene-metabolite network with implemented causality deciphers informational fluxes of sulphur stress response, J. Exp. Bot. 56:1887-1896.

    Article  CAS  PubMed  Google Scholar 

  • Nikolau, B.J., Ohlrogge, J.B., and Wurtele, E.S., 2003, Plant Biotin-Containing Carboxylases, Arch. Biochem. Biophys. 414:211-222.

    Article  CAS  PubMed  Google Scholar 

  • Oliver, D.J., Nikolau, B., and Wurtele, E.S., 2002, Functional genomics: high-throughput mRNA, protein, and metabolite analyses, Metab. Eng. 4:98106.

    Article  Google Scholar 

  • Patton, D.A., Volrath, S., and Ward, E.R., 1996, Complementation of an Arabidopsis thaliana biotin auxotroph with an Escherichia coli biotin biosynthetic gene, Molecular Genetics and Genomics. 251:261-266.

    CAS  Google Scholar 

  • Ratcliffe, R.G., and Shachar-Hill, Y., 2005, Revealing metabolic phenotypes in plants: inputs from NMR analysis, Biol. Rev. Camb. Philos. Soc. 80:27-43.

    Article  CAS  PubMed  Google Scholar 

  • Sriram, G., Fulton, D.B., Iyer, V.V., Peterson, J.M., Zhou, R., Westgate, M.E., Spalding, M.H., and Shanks, J.V., 2004, Quantification of Compartmented Metabolic Fluxes in Developing Soybean Embryos by Employing Biosynthetically Directed Fractional 13C Labeling, Two-Dimensional [13C, 1H] Nuclear Magnetic Resonance, and Comprehensive Isotopomer Balancing, Plant Physiol. 136:3043-3057.

    Article  CAS  PubMed  Google Scholar 

  • Thimm, O., Bläsing, O., Gibon, Y., Nagel, A., Meyer, S., Krüger, P., Selbig, J., Müller, L.A, Rhee, S.Y., and Stitt, M., 2004, Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes, The Plant Journal 37:914-939.

    Article  CAS  PubMed  Google Scholar 

  • Weaver, L.M., Yu, F., Wurtele, E.S., and Nikolau, B.J., 1996, Characterization of the cDNA and gene coding for the biotin synthase of Arabidopsis thaliana, Plant Physiol. 110:1021-1028.

    Article  CAS  PubMed  Google Scholar 

  • Wurtele, E.S., Dickerson, J.D., Cook, D., Hofmann, H., Li, J., and Diao, L.. 2003, MetNet: software to build and model the biogenetic lattice of Arabidopsis, Comp. Funct. Genomics 4:239-245.

    Article  CAS  PubMed  Google Scholar 

  • Xiong, M., Zhao, J., and Xiong, H., 2004, Network-based regulatory pathways analysis, Bio-informatics 20:2056-2066.

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer

About this paper

Cite this paper

Wurtele, E.S. et al. (2007). MetNet: Systems Biology Tools for Arabidopsis. In: Nikolau, B.J., Wurtele, E.S. (eds) Concepts in Plant Metabolomics. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-5608-6_10

Download citation

Publish with us

Policies and ethics