Output | Genetics | Manhattan Plot (Multiple SNP-Trait Analysis)

Manhattan Plot (Multiple SNP-Trait Analysis)
A Manhattan Plot tab with genes grouped by chromosome is shown below:
The Manhattan Plot tab contains the following elements:
When there are multiple annotation plotting groups such as chromosomes, a Manhattan plot is used to show p-values for all genes (or other type of annotation analysis groups) from a particular type of test in a single scatter plot.
The Y -axis variable is the p -value from the association test, converted to the -log or -log 10 scale if selected in the process dialog . The X -axis plots the genes in cumulative order, according to the location of the first SNP in the gene, within and across annotation plotting groups.
Each annotation plotting group is assigned a color that is displayed in a legend below the plots.
A horizontal reference line is drawn as a red, dashed line at the significance level that was specified. For -log or -log 10 -converted p -values, genes above this line are significant; for p -values on the original scale, genes below the line are significant.
A separate plot is created for each association test performed (plots for two different tests are shown above), and if any BY variables were selected, a separate chart is displayed for each BY group as well.
On this plot or any of the other p -value plots, you can mouse-over any of the points on the plot to see the gene's label. When an annotation accession variable is specified when running the process, you can select a point and click on any of the Annotation action buttons - GenBank Nucleotide , UniGene Database , AceView Database , or dbSNP - to link directly to the corresponding website to view extensive annotation information about the gene's first locus .