Overview

Lipid Genie's Lipid Viewer can be used to query mapped Quantitative Trait Loci (QTLs) from the Gene-Guided Lipid Identification manuscript by selecting a specific lipid species.

Logarithm-of-Odds (LOD) and Allele Effect plots for mapped QTLs are visualized in parallel to genes located within a 3 megabase pair window of QTL's apex LOD score.

Genes containing single nucleotide polymorphisms (SNPs) that are associated with a selected QTL are highlighted in orange.
Associated SNPs that are of particular interest to our study are highlighted in red.

How To?

A lipid species can be selected by using the filtering controls provided in the control panel:

Filtering and Selecting Lipid Species

1 - Filter Lipids By Lipid Class

Use the Lipid Class select box under the section of the control panel.
• If a lipid class is specified, Lipid Genie will only offer lipid species belonging to the selected class in the Select a Lipid section of the control panel.

2 - Filter Lipids By Tissue

Lipids and other biomolecules are expressed differently depending on the tissue of origin. Select a tissue type in the Tissue select box under the section of the control panel.
• If a tissue is specified, Lipid Genie will only offer lipid species that were quantified in the selected tissue.

3 - Filter Lipids By Precursor m/z

Specific lipid species may not have been assigned a putative identification in this study due to a variety of reasons. However, we have included all unidentified lipid-like species in this resource to allow other scientists to map lipids of interest to our unknown species using the precursor mass-to-charge ratio.
• Enter a known lipid precursor m/z and mass tolerance into the control panel to filter lipid species.

Selecting a Lipid Species and QTL

Select a Specific Lipid Species

Use the dropdown contained in the Select a Lipid portion of the control panel to select a lipid species. Individual QTLs associated with this lipid are queried by Lipid Genie and placed into a select box below for further interrogation.
• If there are no lipid species which match the filter constraints provided by the user, relax or remove some filters.

Selecting a Quantitative Trait Locus to View

If a selected lipid species is linked to mapped QTLs, they can be selected for visualization using the dropdown contained in the Select A QTL dropdown.
• If no QTLs are associated with this locus, the dropdown will be hidden and you'll be prompted to select another lipid species.

Control Panel

Filter Lipid QTLs

Lipid Class

Tissue

Precursor m/z

Mass tolerance

Select A Lipid:

Select A Lipid Feature: {{lipids.options.filteredIds.length}} Option(s)

No valid lipid ID's found using this filter

Select A QTL to View

Select A QTL: {{lipids.options.qtls.length}} Option(s)

LOD Plot: This visualization displays the calculated Logorithm-of-Odds score for this QTL across the entire chromosome.
Allele Effect Plot: This visualization displays the calculated Founder Strain allele effects for this QTL across the entire chromosome.
• The QTL's genetic locus is indicated at the largest LOD score.

Gene Plot: This visualization displays all MGI mouse genes within a ±1.5 megabase pair window of this selected QTL's apex LOD score.
• Genes which contain a SNP are highlighted in orange.
• Genes which contain a SNP that we consider of particular interest are highlighted in red.
• Pan/zoom functionality is possible using the mouse wheel and click/dragging.

Control Panel

{{chromosomeNumber}}