Visualize Copy Number Alterations in the GDC Data Portal
The GDC released a new version of the GDC Data Portal with new visualization tools for copy number variations (CNVs).
Analyze Data
The NCI GDC Releases New Cohort Comparison Features
The NCI's Genomic Data Commons (GDC) released new features allowing users to build and compare custom cohorts and perform operations on case, gene, or mutation sets.
GDC Webinar: Analyzing Data using GDC Data Analysis, Visualization, and Exploration (DAVE) Tools
The Analyzing Data using GDC Data Analysis, Visualization, and Exploration (DAVE) Tools webinar will help introduce users to GDC tools for analyzing data from cancer genomic studies.
How do I search for a particular mutation?
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To search for a mutation, you can utilize the Quick Search bar at the top right portion of the GDC Portal by entering in either a dbSNP reference cluster ID (rs#) or the coordinates of the chromosomal change. For example entering in 'rs121912651' or 'chr17:g.7674221G>A' will bring the user to the mutation entity page for that mutation.
Why does the GDC display common genes such as TTN that are associated with every cancer in the most frequently mutated genes table?
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The GDC is not normalizing frequency by gene length. This is currently under discussion. As such, these genes are appearing in the mutated genes table. Users can filter by the COSMIC Cancer Gene Census to display only genes for which mutations have been causally implicated in cancer.
On the GDC Project summary page or Mutation Frequency > Gene tab, why are the # of Mutations sometimes less than the # Affected Cases?
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The “# Mutations” column in the Project or Mutation Frequency > Gene tab displays the number of distinct (unique) mutations within the affected cases and not necessarily the total number of all mutations within the project or query filter.
The NCI GDC Officially Launched DAVE: Data Analysis, Visualization, and Exploration
The NCI's Genomic Data Commons (GDC) officially launched Data Analysis, Visualization, and Exploration (DAVE) tools transforming the GDC from a cancer genomics data repository into an interactive k
Where can I find information on the format of GDC MAF Files?
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Please refer to the GDC MAF File Specification to obtain detailed information on the format of GDC MAF files.
Can I use the GDC Application Programming Interface (API) to retrieve data sets associated with visualizations?
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Yes. The GDC provides additional analysis endpoints to retrieve data sets associated with visualizations. Analysis endpoints include: survival, top_cases_counts_by_genes, top_mutated_genes_by_project, top_mutated_cases_by_gene, top_mutated_cases_by_ssm, and mutated_cases_count_by_project.
Please refer to the GDC API User's Guide Analysis Section for additional information.
How is survival analysis calculated?
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