A portion of the
Manhattan Plot
tab is shown below:
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.
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 for each
trait
and the overall
MANOVA
test, 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 marker's label(
SNP ID
, for example). 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
.