Pathways

Pathway maps drawn using Pathway Editor software, plus .path files for editing pathways using Pathway Editor

The Pathway Editor is a program for managing, visualizing, and editing signaling and metabolic pathways. Pathways may be created from scratch, accessed by opening a .path file, or downloaded from the LIPID MAPS website via the Pathway Editor application. Time course graphs for both lipids and genes, and data for technical and biological replicates for lipids can be displayed within the Pathway Editor. For lipids, the Pathway Editor also provides links to KEGG and to LMSD records, with lipid structures and annotations. Links to annotations in GeneEntrez and the Mouse Genome Database are provided for genes.

Please see our Pathway Editor tutorial for an overview of Pathway Editor features, including how to start the Pathway Editor, access LIPID MAPS pathways and display LIPID MAPS and user-provided experimental data, create pathways from scratch, and edit and save pathway files and images. Instructions for working with SBML and BioPAX formats are also provided.

Download and launch Pathway Editor

View pathway maps, download LIPID MAPS pathway (*.path) files, and view time course data for lipids and genes.

• Fatty Acids
  • Pathway maps
    • Arachidonic acid metabolism
    • Omega-3 and omega-6 fatty acids [cells]
    • Omega-3 and omega-6 fatty acids [media]
    • Omega-9 and other fatty acids [cells]
    • Omega-9 and other fatty acids [media]
  • Pathway Editor .path files:
    • Arachidonic acid metabolism Eicosanoids [media]
    • Omega-3 and omega-6 fatty acids [cells]
    • Omega-3 and omega-6 fatty acids [media]
    • Omega-9 and other fatty acids [cells]
    • Omega-9 and other fatty acids [media]
  • Tabular data Eicosanoids [media]
  • Tabular data Fatty acids [cells]
• Glycerolipids and Glycerophospholipids
  • Pathway maps (acyl chains):
    32:0 32:1 34:0 34:1 36:0 36:1 38:0 38:1 38:4
  • Pathway Editor .path files (acyl chains):
    32:0 32:1 34:0 34:1 36:0 36:1 38:0 38:1 38:4
  • Tabular data
• Sphingolipids
  • Pathway maps (N-acyl chains):
    C16:0 C18:0 C20:0 C22:0 C24:0 C24:1 C26:1 C26:2 All N-acyl chain lengths
  • Pathway Editor .path files (N-acyl chains):
    C16:0 C18:0 C20:0 C22:2 C24:0 C24:1 C26:1 C26:2
    All N-acyl chain lengths
  • Tabular data
• Sterol Lipids
  • Pathway map: Biosynthesis of steroids
  • Pathway Editor .path file Biosynthesis of steroids
  • Tabular data

The Workbench uses Java WebStart 1.6 or later version and JOGL(Java Open Graphics Language). Please install Java Web Start if you do not have it already (you can tell you do not have Java Web Start if you get a message when you try to install Pathway Editor). This enables you to run Java applications started from a web page. JOGL is downloaded as part of the Pathway Editor program.

References