Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Nov 1;35(21):4507-4508.
doi: 10.1093/bioinformatics/btz250.

Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data

Geremy Clair  1 , Sarah Reehl  2 , Kelly G Stratton  2 , Matthew E Monroe  1 , Malak M Tfaily  3   4 , Charles Ansong  1 , Jennifer E Kyle  1
Affiliations

Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data

Geremy Clair et al. Bioinformatics. .

Abstract

Summary: Here we introduce Lipid Mini-On, an open-source tool that performs lipid enrichment analyses and visualizations of lipidomics data. Lipid Mini-On uses a text-mining process to bin individual lipid names into multiple lipid ontology groups based on the classification (e.g. LipidMaps) and other characteristics, such as chain length. Lipid Mini-On provides users with the capability to conduct enrichment analysis of the lipid ontology terms using a Shiny app with options of five statistical approaches. Lipid classes can be added to customize the user's database and remain updated as new lipid classes are discovered. Visualization of results is available for all classification options (e.g. lipid subclass and individual fatty acid chains). Results are also visualized through an editable network of relationships between the individual lipids and their associated lipid ontology terms. The utility of the tool is demonstrated using biological (e.g. human lung endothelial cells) and environmental (e.g. peat soil) samples.

Availability and implementation: Rodin (R package: https://github.com/PNNL-Comp-Mass-Spec/Rodin), Lipid Mini-On Shiny app (https://github.com/PNNL-Comp-Mass-Spec/LipidMiniOn) and Lipid Mini-On online tool (https://omicstools.pnnl.gov/shiny/lipid-mini-on/).

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Lipid Mini-On text-mining pipeline. (A) Text-mining process parses lipid names into three distinct objects entitled .intact [e.g. TG(18:0/18:3/20:4)], .allchains (e.g. 56:7) and .chains (e.g. 18:0). (B) Based on the classification in (A) LO terms are mined from the query and universe files and compared for LO enrichment
See this image and copyright information in PMC

References

    1. Chang W. et al. (2018) Shiny: Web Application Framework for R. R Package Version 1.2.0. https://CRAN.R-project.org/package=shiny.
    1. Huang da W. et al. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1–13. - PMC - PubMed
    1. Kyle J.E. et al. (2018) Cell type-resolved human lung lipidome reveals cellular cooperation in lung function. Sci. Rep., 8, 13455. - PMC - PubMed
    1. Kyle J.E. et al. (2017) LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data. Bioinformatics, 33, 1744–1746. - PMC - PubMed
    1. Sud M. et al. (2007) LMSD: lIPID MAPS structure database. Nucleic Acids Res., 35, D527–D532. - PMC - PubMed

Publication types