The GDC Data Portal, Video Guides to the Genomic Data Commons
NIH, National Cancer Institute
gdc.cancer.gov
In this video, we will provide an overview of the Genomic Data Commons data portal,
including information about the data, analysis tools, and different ways to access the data.
The GDC data portal offers various ways to work with cases, genes, and mutations.
and provides exploration tools for visualizing and browsing data
and analysis tools for performing set operations and comparisons.
The home page displays summary information about the data within the GDC
and provides a few navigational elements.
On the projects page, users can review and filter data on a project level.
The page also provides a listing of the most frequently mutated genes and projects
along with a summary that lists the available data for each project.
The exploration page can be used to explore data using custom case, gene, and mutation filters.
For example if i’m only interested in data for TCGA breast cancer patients
and mutations on protein coding genes called by the Mutect2 variant caller
I can add these filters on the left.
As you add filters to the data on the Exploration Page, the Results section will be automatically updated.
Results are divided into four different tabs: Cases, Genes, Mutations, and OncoGrid.
The cases tab summarizes all the cases that meet the filter criteria.
The genes tab summarizes all the genes found to have mutations within the selected cases.
The top of this section contains a bar graph of the most frequently mutated genes
in addition to a survival plot of all the cases.
Below these graphs is a table with information about each of the genes affected.
The Mutations tab summarizes all the mutations identified within the group of selected cases.
The top of this tab is a survival plot
of all the cases within the exploration page filters.
Below is a table of the information about each of the mutations.
The OncoGrid plot gives a visual overview of the most frequently mutated genes and cases
where each row represents one of the frequently mutated genes
and each column one of the cases with mutations
and the colors indicate the different types of consequences resulting from the mutations.
The Analysis page allows you to analyze data from saved cohorts of patients.
For example, you can use the Set Operations
to find a listing of patients that contain both RNA-Seq data and whole exome data
The Repository page allows you to search and directly download data
of various types and formats for analysis outside of the data portal.
For example, you may be interested in finding alignment files associated with male patients having neuroblastoma.
You can see which cases and files satisfy these criteria.
Advanced search is available for building more complex search queries.
The system provides suggestions for both the fields and values
enabling user driven discovery of the available search options.
While anyone can explore the data found in the GDC
most of the genomic data files are controlled access.
To access controlled data you will need to have the correct dbGaP permissions tied to your eRA commons or iTrust account.
Additional information can be found on the website under "Obtaining Access to Controlled Data".
Files can be downloaded individually as well as in bulk by adding them to your cart.
For large or bulk transfer, the GDC recommends using the data transfer tool.
Another powerful capability of the GDC Data Portal is BAM slicing.
This feature allows users to download only the portion of the alignment file that is relevant to their work.
For example, rather than downloading reads related to the entire exome
perhaps you would only like to see reads in a small region of the genome, such as on chromosome 1 from base 1-100,000.
The GDC also maintains a legacy archive containing unharmonized data from earlier NCI programs such as TCGA and TARGET.
The legacy archive has much of the same functionality as the Data Portal
but should be used with care as each project may have been analyzed using different tools
and versions of the human reference genome.
Additional information about the GDC Data Portal, and other components can be found in our documentation.
You will find detailed explanations and examples to help you navigate the GDC Data Portal.
U.S. Department of Health and Human Services
National Institutes of Health, National Cancer Institute
gdc.cancer.gov
support@nci-gdc.datacommons.io
1-800-4-CANCER
Produced February 2018