Skip to main content
SpringerLink
Log in

VANTED: A Tool for Integrative Visualization and Analysis of -Omics Data

  • Protocol
  • First Online:
Plant Membrane Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1696))

Abstract

The investigation of biological systems from different perspectives leads, due to novel -omics technologies, to large-scale, heterogeneous, and complex datasets. To elucidate molecular programs that control biological systems growth and development the integration and analysis of these -omics data remains challenging. Network-integrated visualizations based on graphical standards support intuitive exploration and interpretation of -omics data within the functional context. This integrated vision of the biological system to be studied tries to extract all hidden information for deepening our understanding and reveals new biological insights.

The method described here gives detailed instructions on the generation of such an integrative visualization of -omics data in the context of networks presented in the Systems Biology Graphical Notation (SBGN) using VANTED; a software tool for systems biology applications. An example illustrates the application of the method for metabolomics and proteomics data integration and analysis using a primary metabolic pathway, for the model crop potato.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 119.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 159.99
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

Institutional subscriptions

References

  1. Fukushima A, Kanaya S, Nishida K (2014) Integrated network analysis and effective tools in plant systems biology. Front Plant Sci 5:598–607

    Article  PubMed  PubMed Central  Google Scholar 

  2. Hirai MY, Yano M, Goodenowe DB, Kanaya S, Kimura T, Awazuhara M, Arita M, Fujiwara T, Saito S (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci 101:10205–10210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Fukushima A, Kusano M (2014) A network perspective on nitrogen metabolism from model to crop plants using integrated ‘omics’ approaches. J Exp Bot 65:5619–5630

    Article  CAS  PubMed  Google Scholar 

  4. Hossain MS, Joshi T, Stacey G (2015) System approaches to study root hairs as a single cell plant model: current status and future perspectives. Front Plant Sci 6:363–370

    PubMed  PubMed Central  Google Scholar 

  5. Soni P, Nutan KK, Soda N, Nongpiur RC, Roy S, Singla-Pareek SL, Pareek A (2015) Towards understanding abiotic stress signaling in plants: convergence of genomic, transcriptomic, proteomic, and metabolomic approaches. In: Pandey GK (ed) Elucidation of abiotic stress signaling in plants. Springer, New York

    Google Scholar 

  6. Yoshida T, Mogami J, Yamaguchi-Shinozaki K (2015) Omics approaches toward defining the comprehensive abscisic acid signaling network in plants. Plant Cell Physiol 56:1043–1052

    Article  CAS  PubMed  Google Scholar 

  7. Carneiro JMT, Madrid KC, Maciel BCM, Arruda MAZ (2015) Arabidopsis thaliana and omics approaches: a review. J Integr OMICS 5:1–16

    Article  Google Scholar 

  8. Komatsu S, Shirasaka N, Sakata K (2013) ‘Omics’ techniques and their use to identify how soybean responds to flooding. J Proteome 93:169–178

    Article  CAS  Google Scholar 

  9. Guerriero G, Sergeant K, Hausman JF (2013) Integrated -omics: a powerful approach to understanding the heterogeneous lignification of fibre crops. Int J Mol Sci 14:10958–10978

    Article  PubMed  Google Scholar 

  10. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin A-C (2010) Visualization of omics data for systems biology. Nat Methods 7:S56–S68

    Article  CAS  PubMed  Google Scholar 

  11. Moyano TC, Vidal EA, Contreras-López O, Gutiérrez RA (2015) Constructing simple biological networks for understanding complex high-throughput data in plants. Methods Mol Biol 1284:503–526

    Article  CAS  PubMed  Google Scholar 

  12. Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N (2015) Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative. Front Bioeng Biotechnol 3:19–25

    Article  PubMed  PubMed Central  Google Scholar 

  13. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin I, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Scha JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J (2003) The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524–531

    Article  CAS  PubMed  Google Scholar 

  14. Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem M, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman T, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H (2009) The Systems Biology Graphical Notation. Nat Biotechnol 27:735–741

    Google Scholar 

  15. Moodie S, Le Novère N, Demir E, Mi H, Villéger A (2015) Systems Biology Graphical Notation: Process Description language level 1, version 1.3. J Integr Bioinform 12:263

    Google Scholar 

  16. Sorokin A, Le Novère N, Luna A, Czauderna T, Demir E, Haw R, Mi H, Moodie S, Schreiber F, Villéger A (2015) Systems Biology Graphical Notation: Entity Relationship language level 1, version 2. J Integr Bioinform 12:264

    Google Scholar 

  17. Mi H, Schreiber F, Moodie S, Czauderna T, Demir E, Haw R, Luna A, Le Novère N, Sorokin A, Villéger A (2015) Systems Biology Graphical Notation: Activity Flow language level 1, version 1.2. J Integr Bioinform 12:265

    Google Scholar 

  18. Henry VJ, Bandrowski AE, Pepin A-S, Gonzalez BJ, Desfeux A (2014) OMICtools: an informative directory for multi-omic data analysis. Database 2014:1–5

    Article  Google Scholar 

  19. Rohn H, Junker A, Czauderna T, Hartmann A, Klapperstück M, Treutler H, Grafahrend-Belau E, Klukas C, Schreiber F (2012) VANTED v2: a framework for systems biology applications. BMC Syst Biol 6:139–152

    Article  PubMed  PubMed Central  Google Scholar 

  20. Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S (2012) MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res 40:D1173–D1177

    Article  CAS  PubMed  Google Scholar 

  21. Czauderna T, Klukas C, Schreiber F (2010) Editing, validating, and translating of SBGN maps. Bioinformatics 26:2340–2341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Himsolt M (1996) GML: a portable graph file format. Technical Report, University of Passau

    Google Scholar 

  23. Foyer CH, Noctor G, Hodges M (2011) Respiration and nitrogen assimilation: targeting mitochondria-associated metabolism as a means to enhance nitrogen use efficiency. J Exp Bot 62:1467–1482

    Article  CAS  PubMed  Google Scholar 

  24. Junker A, Rohn H, Czauderna T, Klukas C, Hartmann A, Schreiber F (2012) Creating interactive,web-basedanddata-enrichedmaps using the Systems Biology Graphical Notation. Nat Protoc 7:579–593

    Google Scholar 

Download references

Acknowledgments

Funding of the work of A.M. Jozefowicz by a grant from the Bundesministerium für Ernährung und Landwirtschaft (BMEL) via the Fachagentur Nachwachsende Rohstoffe e.V. (FNR 22023411) is greatfully acknowledged.

Author information

Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

    Anja Hartmann & Anna Maria Jozefowicz

Authors
  1. Anja Hartmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anna Maria Jozefowicz
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Anja Hartmann .

Editor information

Editors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany

    Hans-Peter Mock

  2. Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany

    Andrea Matros

  3. Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany

    Katja Witzel

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media LLC

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Hartmann, A., Jozefowicz, A.M. (2018). VANTED: A Tool for Integrative Visualization and Analysis of -Omics Data. In: Mock, HP., Matros, A., Witzel, K. (eds) Plant Membrane Proteomics. Methods in Molecular Biology, vol 1696. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7411-5_18

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-7411-5_18

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7409-2

  • Online ISBN: 978-1-4939-7411-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation