LION/web: a web-based ontology enrichment tool for lipidomic data analysis

  1. Martijn R Molenaar
  2. Aike Jeucken
  3. Tsjerk A Wassenaar
  4. Chris H A van de Lest
  5. Jos F Brouwers
  6. J Bernd Helms

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Abstract

Background

A major challenge for lipidomic analyses is the handling of the large amounts of data and the translation of results to interpret the involvement of lipids in biological systems.

Results

We built a new lipid ontology (LION) that associates >50,000 lipid species to biophysical, chemical, and cell biological features. By making use of enrichment algorithms, we used LION to develop a web-based interface (LION/web, www.lipidontology.com) that allows identification of lipid-associated terms in lipidomes. LION/web was validated by analyzing a lipidomic dataset derived from well-characterized sub-cellular fractions of RAW 264.7 macrophages. Comparison of isolated plasma membranes with the microsomal fraction showed a significant enrichment of relevant LION-terms including “plasma membrane", “headgroup with negative charge", "glycerophosphoserines", “above average bilayer thickness", and “below average lateral diffusion". A second validation was performed by analyzing the membrane fluidity of Chinese hamster ovary cells incubated with arachidonic acid. An increase in membrane fluidity was observed both experimentally by using pyrene decanoic acid and by using LION/web, showing significant enrichment of terms associated with high membrane fluidity ("above average", "very high", and "high lateral diffusion" and "below average transition temperature").

Conclusions

The results demonstrate the functionality of LION/web, which is freely accessible in a platform-independent way.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giz061

    Martijn R. Molenaar §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Martijn R. MolenaarAike Jeucken §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteTsjerk A. Wassenaar ‡Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteChris H. A. van de Lest §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJos F. Brouwers §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJ. Bernd Helms §Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, 3584 CM, Utrecht, The NetherlandsFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteFor correspondence: J.B.Helms@uu.nl

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giz061 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.101733 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.101734 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.101735

  2. Version published to 10.1093/gigascience/giz061
  3. Version published to 10.1101/398040v2 on bioRxiv
  4. Version published to 10.1101/398040v1 on bioRxiv