cBioPortal Tutorial #1:
Single Study Exploration
Explore all data in a dataset
Last update: December 21, 2021
Tutorial Objectives
cBioPortal Main Page
Browse available datasets and select studies to explore or query
Number of studies for each tissue of origin (click to filter)
List of all studies, organized by organ system
Search studies
Link to this page
Selecting a study: from Query
1. Filter the list of studies (optional)
3. Or click on “View study summary” button
2. Select the checkbox next to the study of interest and click “Explore Selected Studies”
Link to this page
Selecting a study: from Data Sets page
3. Click on data set of interest
1. Use search functionality to find datasets of interest
Link to this page
2. Or sort by number of samples with each data type
Once you select a study by either method
you land on the Study Summary Tab.
Here you can explore features (e.g. mutated genes or gender) of the samples in the study (or of a subset of samples in the study) or initiate a query.
The features available to explore will depend on the data available for the particular study selected.
Study Summary Tab: Overview
Study summary provides an interactive overview of the study for exploration. Individual charts can be used to select a subset of the samples. All charts will then update to reflect the features of that subset.
Link to this page
Study Summary Tab: Charts
Hover for a description of the data in this chart.
Click to convert the pie chart to a table. Note that hovering over the chart will also bring up a tooltip with tabular data.
Click to go to a group comparison session with groups based on these values. See the group comparison tutorial for more details.
Click to remove this chart from view.
Click to download data (text file) or plot (PDF or SVG).
Hover over this button to bring up a menu with the options below:
Click and drag to resize a chart
Link to this page
Hover over a chart to find these buttons
Click and drag on the grey bar with the chart name to move a chart
Study Summary Tab: Charts
Genomic: lists charts summarizing genomic data
Link to this page
Add charts using this button. Added charts can be used like any other chart to filter or define groups for comparison.
Clinical: lists all patient- and sample-level data available for this study
Gene Specific: add charts for individual genes from any molecular profile with continuous data, e.g. mRNA expression.
Study Summary Tab: Charts
Custom Data: add charts with new data for the existing samples, for example results of your own analysis that classifies TCGA samples into groups.
Link to this page
Arm-level CNA, Microbiome Signature and others: add charts for additional datatypes that are available for some studies. Not all studies will have these subtabs.
X vs Y: add charts comparing two clinical attributes. Note this feature is still under development.
Study Summary Tab: Selecting subsets of data
1. You can use any chart or plot to select a subset of samples. Here, IDH1 mutated samples are selected.
4. To remove filters, click on the blue arrow to remove the filter from a specific chart. Or, use the “Clear All Filters” button in the header.
2. All plots update to include just the samples with IDH1 mutations. You can also apply additional filters and plots will continue to update.
3. After applying filters, this button will generate a shareable link with the filters applied.
Link to this page
Clinical Data Tab
Scroll to the right to see more columns. Each column can be sorted by clicking on the column header.
Link to this page
Filters applied in the Summary tab apply to this table
Show additional data (available data will vary based on the study)
Download clinical data table
CN Segments Tab
Enter a gene name or genomic coordinates
Link to this page
Filters applied in the Summary tab also apply to this tab
When copy number data is available, this tab integrates the Integrated Genomics Viewer (IGV) to allow browsing of copy number data across the entire genome. Each row is a single sample.
Additional Tabs: Heatmaps
This tab will only appear for some TCGA studies. It is an embedding of the Next-Generation Clustered Heat Map interactive heatmap tool.
Link to this page
Study View: Additional Features
Click here to see all selected samples/patients in Patient View.
See tutorial.
Link to this page
Click here for group comparison. See tutorial.
Click here to create a virtual study of the selected samples/patients.
See tutorial.
Use this box to run a query (see next slide).
Click here to enter a list of sample or patient IDs for a custom filter.
Study Summary Tab: Run a query
3. Or click on a gene to add it to the query
2. Type a gene name here
Link to this page
1. Apply filters (optional). Here, we are filtering to samples that have both mutation and copy number data. The query will run in only these selected samples.
3. Then click here to run the query
See Tutorial #2: Single Study Query
Questions?
Check out our other tutorials
or email us at: cbioportal@googlegroups.com