Bioinformatics strategies for the analysis of lipids

Craig E. Wheelock, Susumu Goto, Laxman Yetukuri, Fabio Luiz D'Alexandri, Christian Klukas, Falk Schneiber, Matej Orešič

Research output: Chapter in Book/Report/Conference proceedingChapter or book articleScientificpeer-review

23 Citations (Scopus)

Abstract

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.
Original languageEnglish
Title of host publicationLipidomics
Subtitle of host publicationMethods and Protocols
EditorsDonald Armstrong
PublisherHumana Press
Pages339-368
Volume2
ISBN (Electronic)978-1-60761-325-1
ISBN (Print)978-1-60761-324-4
DOIs
Publication statusPublished - 2009
MoE publication typeA3 Part of a book or another research book

Publication series

NameMethods in Molecular Biology
Volume580
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

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Computational Biology
Lipids
Genome
Databases
Encyclopedias
Informatics
Information Services
Research
Software
Pathology
Genes
Proteins

Keywords

  • Bioinformatics
  • lipid
  • lipidomics
  • pathway reconstruction
  • KEGG
  • KGML-ED
  • VANTED
  • MZmine
  • lipidDB

Cite this

Wheelock, C. E., Goto, S., Yetukuri, L., D'Alexandri, F. L., Klukas, C., Schneiber, F., & Orešič, M. (2009). Bioinformatics strategies for the analysis of lipids. In D. Armstrong (Ed.), Lipidomics : Methods and Protocols (Vol. 2, pp. 339-368). Humana Press. Methods in Molecular Biology, Vol.. 580 https://doi.org/10.1007/978-1-60761-325-1_19
Wheelock, Craig E. ; Goto, Susumu ; Yetukuri, Laxman ; D'Alexandri, Fabio Luiz ; Klukas, Christian ; Schneiber, Falk ; Orešič, Matej. / Bioinformatics strategies for the analysis of lipids. Lipidomics : Methods and Protocols. editor / Donald Armstrong. Vol. 2 Humana Press, 2009. pp. 339-368 (Methods in Molecular Biology, Vol. 580).
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Wheelock, CE, Goto, S, Yetukuri, L, D'Alexandri, FL, Klukas, C, Schneiber, F & Orešič, M 2009, Bioinformatics strategies for the analysis of lipids. in D Armstrong (ed.), Lipidomics : Methods and Protocols. vol. 2, Humana Press, Methods in Molecular Biology, vol. 580, pp. 339-368. https://doi.org/10.1007/978-1-60761-325-1_19

Bioinformatics strategies for the analysis of lipids. / Wheelock, Craig E.; Goto, Susumu; Yetukuri, Laxman; D'Alexandri, Fabio Luiz; Klukas, Christian; Schneiber, Falk; Orešič, Matej.

Lipidomics : Methods and Protocols. ed. / Donald Armstrong. Vol. 2 Humana Press, 2009. p. 339-368 (Methods in Molecular Biology, Vol. 580).

Research output: Chapter in Book/Report/Conference proceedingChapter or book articleScientificpeer-review

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AU - Wheelock, Craig E.

AU - Goto, Susumu

AU - Yetukuri, Laxman

AU - D'Alexandri, Fabio Luiz

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AU - Schneiber, Falk

AU - Orešič, Matej

PY - 2009

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N2 - 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.

AB - 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.

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KW - pathway reconstruction

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KW - KGML-ED

KW - VANTED

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KW - lipidDB

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DO - 10.1007/978-1-60761-325-1_19

M3 - Chapter or book article

SN - 978-1-60761-324-4

VL - 2

T3 - Methods in Molecular Biology

SP - 339

EP - 368

BT - Lipidomics

A2 - Armstrong, Donald

PB - Humana Press

ER -

Wheelock CE, Goto S, Yetukuri L, D'Alexandri FL, Klukas C, Schneiber F et al. Bioinformatics strategies for the analysis of lipids. In Armstrong D, editor, Lipidomics : Methods and Protocols. Vol. 2. Humana Press. 2009. p. 339-368. (Methods in Molecular Biology, Vol. 580). https://doi.org/10.1007/978-1-60761-325-1_19