Compare Cohorts
You can compare up to four previously created individual cohorts, to view differences in variants and mutations, RNA expression, copy number variation, and distribution of clinical attributes. Once comparisons are created, they are saved in the Comparisons
left-navigation tab of the Cohorts module.
Create a comparison view
Select
Cohorts
from the left-navigation panel.Select 2 to 4 cohorts already created. If you have not created any cohorts, See Create a Cohort documentation.
Click
Compare Cohorts
in the right-navigation panel.Note you are now in the
Comparisons
left-navigation tab of the Cohorts module.In the
Charts
Section, if theCOHORTS
item is not displayed, click the gear icon in the top right and addCohorts
as the first attribute and clickSave
.The
COHORTS
item in the charts panel will provide a count of subjects in each cohort and act as a legend for color representation throughout comparison screens.For each clinical attribute category, a bar chart is displayed. Use the gear icon to select attributes to display in the charts panel.
You can share a comparison with other team members in the same ICA Project. Please refer to the section on "Sharing a Cohort" on "Create a Cohort" for details on sharing, unsharing, deleting, and archiving, which are analogous for sharing comparisons.
Attribute Comparison
Select the
Attributes
tabAttribute categories are listed and can be expanded using the down-arrows next to the category names. The categories available are based on cohorts selected. Categories and attributes are part of the ICA Cohorts metadata template that map to each Subject.
For example, use the drop-down arrow next to
Vital status
to view sub-categories and frequencies across selected cohorts.
Variants Comparison
Select the
Genes
tabSearch for a gene of interest using its HUGO/HGNC gene symbol
Variants and mutations will be displayed as one needle plot for each cohort that is part of the comparison (see Cohort analysis -> Genes in this online help for more details)
As additional filter options, you can view only those variants that are occur in every cohort; that are unique to one cohort; that have been observed in at least two cohorts; or any variant.
Survival Summary
Select the
Survival Summary
tab.Attribute categories are listed and can be expanded using the down-arrows next to the category names.
Select the drop-down arrow for
Therapeutic interventions
.In each subcategory there is a sum of the subject counts across select cohorts.
For each cohort, designated by a color, there is a
Subject count
andMedian survival (years)
column.Type
Malignancy
in the Search Box and an auto-complete dropdown suggests three different attributes.Select
Synchronous malignancy
and the results are automatically opened and highlighted in orange.
Survival Comparison
Click
Survival Comparison
tab.A Kaplan-Meier Curve is rendered based on each cohort.
P-Value Displayed at the top of Survival Comparison indicates whether there is statistically significant variance between survival probabilities over time of any pair of cohorts (CI=0.95).
When comparing two cohorts, the P-Value is shown above the two survival curves. For three or four cohorts, P-Values are shown as a pair-wise heatmap, comparing each cohort to every other cohort.
Marker Frequency Comparison
Select the
Marker Frequency
tab.Select either
Gene expression
(default),Somatic mutation
, orCopy number variation
For gene expression (up- versus down-regulated) and for copy number variation (gain versus loss), Cohorts will display a list of all genes with bidirectional barcharts
For somatic mutations, the barcharts are unidirectional and indicate the percentage of samples with a mutation in each gene per cohort.
Bars are color-coded by cohort, see the accompanying legend.
Each row shows P-value(s) resulting from pairwise comparison of all cohorts. In the case of comparing two cohorts, the numerical P-value will be displayed in the table. In the case of comparing three or more cohorts, the pairwise P-values are shown as a triangular heatmap, with details available as a tooltip.
Correlation Comparison
Select the
Correlation
tab.Similar to the single-cohort view (
Cohort Analysis | Correlation
), choose two clinical attributes and/or genes to compare.Depending on the available data types for the two selections (categorical and/or continuous), Cohorts will display a bubble plot, violin plot, or scatter plot.
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