The GDC - Custom Set Analysis
Video Guide for the Genomic Data Commons
NIH - National Cancer Institute - gdc dot cancer dot gov
The GDC has many features for analyzing, accessing, and submitting data.
In this video, we will demonstrate some of the data analysis features
available for working with sets. Including creating custom sets,
of cases genes and mutations, managing these sets,
and after you have created sets: comparing cohorts,
and performing set operations.
I will demonstrate the process of custom set analysis in a few examples in the GDC Portal.
In this example, I want to review the differences between patients with mutations in BRCA1 versus BRCA2.
To do so, I can navigate to the Exploration page from the main GDC Portal.
Here i’ll create my first cohort of patients.
I choose TCGA-BRCA as the project and add a gene filter for BRCA1.
On the right you can see that a total of 28 cases in this set have mutations on the BRCA1 gene.
This set is ready to be saved.
To save the set, you click on the button labelled 'Save/Edit Case Set' below the pie chart.
Here i’ll append the name with BRCA1 and click save.
Creating the second set is the same.
I’ll delete the gene filter and add a new filter for BRCA2 and save this set.
We can now manage the sets by clicking the icon named ‘Manage Sets’ at the top.
Here you’ll see the listing of saved sets - including the two new sets that I added just now.
From here you can upload additional sets manually, export, delete sets
and even navigate to the files within the set using the links on the right.
To review these newly created sets you can navigate to the ‘Analysis’ tab at the top.
Here I want to compare the data between these two cohorts, so I’ll choose Cohort Comparison
pick the two sets, and click the ‘Run’ button to do the analysis.
On this page you’ll see various summary statistics between the two cohorts.
We can return to the Analysis page to run another analysis on a couple sets that were saved previously.
In this example, I want to find a listing of the cases that have files for both whole exome and RNA-Seq data for the BRCA project.
I can use set operations to find these cases.
I will choose the two sets of patients with these filters and click the ‘Run’ button on the ‘Set Operations’ page.
On this page you can see that between all the patients, 1044 contain data for both of these experimental strategies.
Clicking on the number of items link will bring me to the Repository page where I can download the files of interest.
More information about the GDC Portal including custom cohort analysis can be found on the GDC Documentation site.
U.S. Department of Health and Human Services
National Institutes of Health / National Cancer Institute
gdc dot cancer dot gov
support at nci dash gdc dot datacommons dot io
1-800-4-CANCER
Produced January 2018