CNV Distribution
CNV Distribution Usage View distribution of copy-number variation (CNV) frequencies across groups
Input
A gene name
A (categorical) Group By column
Notes
Optionally, apply sample filters (right panel) to perform sub-cohort analysis.
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CNV Genes
CNV Genes Usage A table view showing sample counts of copy-number-variation (CNV) for a gene within each CNV category (Amplification, Gain, Neutral, Deletion, and Deep Deletion, commonly derived from GISTIC2 pipelines).
Input
None Notes
Clicking column header will sort rows based on that column. Optionally, apply filters (right pannel) to obtain statistics based on a subset of samples.
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Expression Grouping
Expression Grouping Usage Boxplot view compares median and overall distribution of gene expression levels between groups.
Input
A gene name
A (categorical) Group By column
Notes
For other data types besides gene expression, go to Correlation view.
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Expression Heatmap
Expression Heatmap Usage A heatmap view of gene expression levels for a set of genes.
Input
A list of genes Notes
Gene expression values are scaled to mean 0 and variance of 1 before a filter is applied.
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Expression Volcano
Expression Volcano Usage A volcano view of P-values v.s. Fold-change for comparison data.
Input
Comparison: select a contrast from a comparison analysis (e.g. Tumor vs Normal) Notes
The volcano view only appears for the projects with comparison data.
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Expression Waterfall
Expression Waterfall Usage View sorted gene expression levels colored by a group
Input
A gene name
A (categorical) Group By column
Notes
For other data types besides gene expression, go to Correlation view.
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Methylation Beta Values
Methylation Beta Values Usage View methylation beta value distribution grouped by a column in metadata
Input
Select a probe by typing a gene name
A (categorical) Group By column
Notes
Optionally, apply a sample filter to view distribution from a subset of samples.
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Alteration Distribution
Alteration Distribution Usage View mutation and copy-number variation (CNV) frequencies across groups
Input
A gene name
A (categorical) Group By column
Notes
For CNV data, only Amplification and Deep deletion are shown
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Mutated Genes
Mutated Genes Usage A table view showing statistic (sample counts and frequencies) of mutated genes in this project.
Input
None Notes
Clicking column header will sort rows based on that column. Optionally, apply filters (right pannel) to obtain statistics based on a subset of samples.
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Mutation Landscape
Mutation landscape view Usage This view displays the mutation location and frequency within a protein domain or region.
Input
A gene name Options
Mouse-over the big circle with numbers in it shows a pop-up box describing the mutation location and associated mutation frequencies.
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Data Availability
Data Availability Usage A table view showing data availability of each sample for each data type.
Input
None Notes
Clicking column header will sort rows based on that column. Optionally, apply filters (right pannel) to select a subset of samples.
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Sample Details
Sample Details Usage Sample details view shows a table view of sample metadata.
Input
None Notes
Click “Select Columns” to pick and display your columns of interests. Clicking column header will sort rows based on that column.
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Sample Grouping
Sample Grouping Usage Sample grouping view shows a stackbar chart based on a grouping and a stacking variable/column in the sample metadata.
Input
A (categorical) Stack By column
A (categorical) Group By column
Notes
Optionally check Sample Grouping (Grouped Bar) (on bottom-left) for related plots.
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Waterfall Plot
Waterfall view Usage View sorted numeric levels colored by a group
Input
Select a data type and input a feature name (e.g. a gene)
A (categorical) Group By column
Notes
For gene expression waterfall plot, simply click Expression > Expression Waterfall view.
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Correlation
Correlation view Usage Input: select features for X- and Y- axis
Options
Add multiple charts by clicking Add on the top-left corner. Selecting points in one chart also (1) highlights the same samples in the remaining charts, and (2) shows the sample table below the charts. To unselect points, select an empty region in a chart.
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Grid Pattern
Grid view Usage Input
On the left panel, three (3) types of data features can be added.
DNA alternation (including mutation, CNV, and fusion) Gene expression Clinical data Options
Double-clicking a feature name re-orders columns (i.e. samples) by the values of that feature. The order of the individual feature (within a feature type) can be re-arranged by changing the feature order in the input field. Clicking Show details displays a ‘zoom-in’ view.
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Survival
Survival view Usage Survival view shows the curves constructed on time-to-event data, where subjects are often stratified by a grouping variable.
The survival plot measures the fraction of patients living for a certain amount of time after event occurs.
Input
Patients can be stratified by gene expression levels or mutation status.
A gene name Select “By Gene Expression” or “By Mutation”. Select a percentile threshold if “By Gene Expression” was selected.
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