Lipidome Projector

Lipidome Projector is a web-based tool for the interactive visualization, exploration and analysis of lipidomics datasets.

A neural network model was used to compute a vector space on a large set of lipid structures taken from the Lipid Maps Structure Database [1] and SwissLipids [2].

User lipidomes are matched by notation and projected onto this space, to be displayed as compact 2D / 3D scatter plots, which allow a quick overview over the distributions of abundances across lipidome samples and lipid classes.

Fully interactive plots, data grids and data processing operations (sorting, filtering, averaging of samples and fold change computation) facilitate an interactive exploration of datasets to find and display structural patterns in lipid abundances.

Availability

Lipidome Projector is currently in active development. It is an open-source Python package available under the MIT license.

A preliminary test-server is available, where users may upload and analyse their own lipidomics data, or familiarize themselves with the software by exploring one of the development datasets [3,4,5].

Currently, a preprint [6] is published and a corresponding journal article is in revision.

References

[1] Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, et al. LMSD: LIPID MAPS structure database. Nucleic Acids Res. 2007;35: D527--D532. doi:10.1093/nar/gkl838

[2] Aimo L, Liechti R, Hyka-Nouspikel N, Niknejad A, Gleizes A, Götz L, et al. The SwissLipids knowledgebase for lipid biology. Bioinformatics. 2015;31: 2860--2866. doi:10.1093/bioinformatics/btv285

[3] Carvalho M, Sampaio JL, Palm W, Brankatschk M, Eaton S, Shevchenko A. Effects of diet and development on the Drosophila lipidome. Mol Syst Biol. 2012;8. doi:10.1038/msb.2012.29

[4] Ejsing CS, Sampaio JL, Surendranath V, Duchoslav E, Ekroos K, Klemm RW, et al. Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry. Proc Natl Acad Sci U S A. 2009;106. doi:10.1073/pnas.0811700106

[5] Lunding LP, Krause D, Stichtenoth G, Stamme C, Lauterbach N, Hegermann J, et al. LAMP3 deficiency affects surfactant homeostasis in mice. PLoS Genet. 2021;17. doi:10.1371/journal.pgen.1009619

[6] Olzhabaev T, Müller L, Krause D, Schwudke D, Torda AE. Lipidome visualisation, comparison, and analysis in a vector space. bioRxiv 2024, doi:10.1101/2024.08.02.606134

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