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LimeMap

Summary

LimeMap is a manually curated map of omega-3- and omega-6-derived lipid-mediator metabolism that can display experimental abundance changes in pathway context. The published release contains editable SBML/CellDesigner and VANTED files, enabling analysts to overlay measured mediators while retaining links to enzymes, receptors, ion channels, and the literature [1].

Coverage and Representation

The initial map contains 282 factors—222 lipid mediators or related metabolites and 60 enzymes, receptors, or ion channels—connected by 279 reactions curated from 102 studies. It includes arachidonic-acid-derived prostaglandins, leukotrienes, HETEs, and EETs as well as omega-3-derived resolvins and maresins [1].

LimeMap is represented as Systems Biology Markup Language (SBML) and visualized with Systems Biology Graphical Notation in CellDesigner. A VANTED-compatible GML version is also provided; both formats allow users to modify the map and overlay their own quantitative data [1].

Demonstration Study

The authors profiled plasma from male C57BL/6J mice two hours after intraperitoneal polyI:C or saline treatment. Of 158 assayed mediators, 66 were detected; all but five targets in the assay panel could be mapped. The visualization showed higher arachidonic-acid-derived signals and lower linoleic-acid-, EPA-, and DHA-derived signals after polyI:C, including increases in PGD2/PGE2 pathways, although the authors explicitly noted that not every displayed change was statistically significant [1].

Limitations

  • The initial release is concentrated on omega-3 and omega-6 pathways and does not cover every bioactive lipid class.
  • Mouse gene symbols are used; human and mouse lipoxygenase activities differ in relevant cases, so cross-species interpretation requires care.
  • Pathway overlay aids interpretation but does not turn a non-significant metabolite change into evidence of regulation.
  • The map requires continuing curation as pathway knowledge changes [1].

Citations

[1] Nishi et al. 2021. LimeMap: a comprehensive map of lipid mediator metabolic pathways. Supports: Map construction, coverage, formats, species caveats, polyI:C experiment, visualization results, and limitations. Location: Abstract; Development and Characteristics of LimeMap; Analysis of the Lipid Mediator Profile; Methods; Code Availability.