Lipid Genie's Gene Viewer can be used to query mapped Quantitative Trait Loci (QTLs) from the Gene-Guided Lipid Identification manuscript by selecting a specific genetic locus.
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.
A specific genetic locus can be selected by one of two ways:
(1) Selecting a gene.
(2) Manually entering a genetic locus.
1 - Selecting a Gene
Filter QTLs By Gene Name
1 - Enter a mouse gene name that you would like to query in the Enter A Gene Name to Query text box under the section of the control panel.
• Lipid Genie will query genes with names that match the entered descriptor to populate the Select a Queried Gene dropdown.
• If more than 200 genes are matched using the entered descriptor, the gene list will be truncated to the top 200 hits.
• Search results can be further refined by providing a more specific gene name.
2 - An exact gene can be selected by using the Select a Queried Gene dropdown.
• The selected gene's chromosome and position (in Mbp) will autopopulate fields in the Filter By Genetic Locus.
• This gene's genetic locus will then be used to query all mapped QTLs within a ±1.5 Mbp window of this locus.
2 - Selecting a Genetic Locus
Filter by Genetic Location
QTL's can also be queried by directly entering a genetic locus using the Chromosome and Position fields.
• Mapped QTLs from our data source within a ±1.5 Mbp window of the entered locus are returned to LipidGenie for investigation.
Selecting a Quantitative Trait Locus to View
If a selected genetic locus contains 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 prompt you to select another locus.
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.