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Lipidomics pp 339-368 | Cite as

Bioinformatics Strategies for the Analysis of Lipids

  • Craig E. Wheelock
  • Susumu Goto
  • Laxman Yetukuri
  • Fabio Luiz D’Alexandri
  • Christian Klukas
  • Falk Schreiber
  • Matej Orešič
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 580)

Summary

Owing to their importance in cellular physiology and pathology as well as to recent technological advances, the study of lipids has reemerged as a major research target. However, the structural diversity of lipids presents a number of analytical and informatics challenges. The field of lipidomics is a new postgenome discipline that aims to develop comprehensive methods for lipid analysis, necessitating concomitant developments in bioinformatics. The evolving research paradigm requires that new bioinformatics approaches accommodate genomic as well as high-level perspectives, integrating genome, protein, chemical and network information. The incorporation of lipidomics information into these data structures will provide mechanistic understanding of lipid functions and interactions in the context of cellular and organismal physiology. Accordingly, it is vital that specific bioinformatics methods be developed to analyze the wealth of lipid data being acquired. Herein, we present an overview of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and application of its tools to the analysis of lipid data. We also describe a series of software tools and databases (KGML-ED, VANTED, MZmine, and LipidDB) that can be used for the processing of lipidomics data and biochemical pathway reconstruction, an important next step in the development of the lipidomics field.

Key words

Bioinformatics Lipid Lipidomics Pathway reconstruction KEGG KGML-ED VANTED MZmine LipidDB 

Notes

Acknowledgments

This research was supported by the Åke Wibergs Stiftelse, the Fredrik and Ingrid Thurings Stiftelse, and The Royal Swedish Academy of Sciences. C.E.W. was supported by a fellowship from the Centre for Allergy Research.

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Craig E. Wheelock
    • 1
    • 2
  • Susumu Goto
    • 2
  • Laxman Yetukuri
    • 3
  • Fabio Luiz D’Alexandri
    • 1
    • 4
  • Christian Klukas
    • 5
  • Falk Schreiber
    • 6
  • Matej Orešič
    • 3
  1. 1.Department of Medical Biochemistry and Biophysics, Division of Physical Chemistry IIKarolinska InstitutetStockholmSweden
  2. 2.Bioinformatics Center, Institute for Chemical ResearchKyoto UniversityKyotoJapan
  3. 3.VTT Technical Research Centre of FinlandEspooFinland
  4. 4.Department of Parasitology, Department of Biochemical SciencesUniversity of San PauloSan PauloBrazil
  5. 5.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  6. 6.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben and Institute of Computer Science, Martin-Luther-UniversityHalle-WittenbergGermany

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