Cohort Analysis
From the Cohorts menu in the left hand navigation, select a cohort created in
Create Cohort
to begin a cohort analysis.The query details can be accessed by clicking the triangle next to
Show Query Details
. The query details displays the selections used to create a cohort. The selections can be edited by clicking the pencil
icon in the top right.- 1.
Charts
will be open by default. If not, clickShow Charts
. - 2.Use the gear icon in the top-right to change viewable chart settings.
- 3.There are four charts available to view summary counts of attributes within a cohort as histogram plots.
- 4.Click
Hide Charts
to hide the histograms.
- 1.By Default, the
Subjects
tab is displayed. - 2.The
Subjects
tab with all Subjects list is displayed belowCharts
with a link to each Subject by ID and other high-level information. By clicking a subject ID, you will be brought to the data collected at the Subject level. - 3.Search for a specific subject, but typing the Subject ID into the
Search Subjects
text box. - 4.Get all details available on a subject by clicking the hyperlinked Subject ID in the Subject list.
- 1.Click the
Marker Frequency
tab, then click theGene Expression
tab. - 2.Down-regulated genes are displayed in blue and Up-regulated genes are displayed in red.
- 3.A frequency in the Cohort is displayed and the Matching number/Total is also displayed in the chart.
- 4.Genes can be searched by using the
Search Genes
text box.
- 1.You are brought to the
Gene
tab under theGene Summary
sub-tab. - 2.Select a Gene by typing the gene name into the
Search Genes
text box. - 3.A
Gene Summary
will be displayed that lists information and links to public resources about the selected gene. - 4.Click the
Variants
tab andShow legend and filters
if it does not open by default. - 5.Below the interactive legend you see a set of analysis tracks: Needle Plot, Primate AI, Pathogenic variants, and Exons.
- 6.The Needle Plot allows toggling the plot by
gnomAD frequency
andSample Count
. SelectSample Count
in thePlot by
legend above the plot. - 7.Hover over the Variant to see details about the Variant from public resources and counts of variants in the selected cohort by disease category.
- 8.Use the Exon zoom bar from each end of the Amino Acid sequence to zoom in on the gene domain to better separate observations.
- 9.The
Pathogenic Variant
Track shows pop up details with pathogenicity calls, phenotypes, submitter and a link to the ClinVar entry is seen by hovering over the purple triangles. - 10.The
Gene Expression
tab shows known gene expression data from tissue types in GTEx. - 11.The
Genetic Burden Test
will only be available forde novo
variants only.
For every correlation, subjects contained in each count can be viewed by selecting the count on the bubble or the count on the X-axis and Y-axis.
- 1.Click the
Correlation
Tab. - 2.In
X-axis category
, selectClinical
. - 3.In
X-axis Attribute
, select a clinical attribute. - 4.In
Y-axis category
, selectClinical
. - 5.In
Y-Axis Attribute
, select another clinical attribute. - 6.You will be shown a bubble plot comparing the first clinical attribute on the x-axis to second attributes on the y-axis.
- 7.The size of the bubbles correspond to the number of subjects falling into those categories.
To see a breakdown of Somatic Mutations vs. RNA Expression levels perform the following steps:
Note this comparison is for a Cancer case.
- 1.Click the
Correlation
Tab. - 2.In
X-axis category
, selectSomatic
. - 3.In
X-axis Attribute
, select a gene. - 4.In
Y-axis category
, selectRNA expression
. - 5.In
Y-Axis Attribute
, type a gene and leaveReference Type
,NORMAL
. - 6.Click
Continuous
to see violin plots of compared variables.
Note this comparison is for a Cancer case.
- 1.Click the
Correlation
Tab. - 2.In
X-axis category
, selectSomatic
. - 3.In
X-axis Attribute
, type a gene name. - 4.In
Y-axis category
, selectClinical
. - 5.In
Y-Axis Attribute
, select a clinical attribute.
- 1.Click the
Molecular Breakdown
Tab. - 2.In
Enter a clinical Attribute
, and select a clinical attribute. - 3.In
Enter a gene
, select a gene by typing a gene name. - 4.You are shown a stacked bar-chart by the clinical attribute selected values on the Y-axis.
- 5.For each attribute value the bar represents the % of Subjects with
RNA Expression
,Somatic Mutation
, andMultiple Alterations
.
If there is Copy Number Variant data in the cohort:
- 1.Click the
CNV
tab. - 2.A graph will show CNV a Sample Percentage on the Y-axis and Chromosomes on the X-axis.
- 3.Any value above Zero is a copy number gain, and any value below Zero is a copy number loss.
- 4.Click
Chromosome:
to select a specific chromosome position.
ICA allows for integrated analysis in a computation workspace. You can export your cohorts definitions and, in combination with molecular data in your ICA Project Data, perform, for example, a GWAS analysis.
- 1.Confirm the VCF data for your analysis is in ICA Project Data.
- 2.
- 3.Navigate back to ICA Cohorts.
- 4.
- 5.From the
Subjects
Tab click theExport subjects...
from the top-right of the subject list. The file can be downloaded to the Browser or ICA Project Data. - 6.We suggest using export
...to Data Folder
for immediate access to this data in Bench or other areas of ICA. - 7.Create another cohort if needed for your Research and complete the last 3 steps.
- 8.Navigate to the Bench workspace created in the second step.
- 9.After the workspace has started up, click
Access
. - 10.Find the
/Project/
folder in the Workspace file navigation. - 11.This folder will contain your cohort files created along with any pipeline output data needed for your workspace analysis.
Last modified 1d ago