TCGA Copy Number Portal (TCGA)

This portal is designed to facilitate the use and understanding of high resolution copy number data amassed from cancer samples in the TCGA. All data in this portal were generated at the Broad Institute TCGA Genome Characterization Center. This portal is modeled after Tumorscape which contains copy number data from non-TCGA projects (Beroukhim et al., 2010).


Gene-Centric GISTIC Analyses

Genes (including miRNAs) can be individually queried by Gene Symbol here. The available data include:

  1. A summary statement of the significance of copy number alterations affecting that gene or transcript.
  2. For amplifications and deletions separately, a table representing the results of GISTIC analyses pertaining to that gene across the entire dataset and within cancer types that are well-represented in the dataset.
  3. Clicking on the chromosome region links displayed on the analyses pages will launch the Integrative Genomics Viewer (IGV) on the data for that region.

More details on available analyses    More details on gene-centric analyses    Explore data by gene now


Cancer-Centric GISTIC Analyses

Cancer types can be individually queried here. The available data include:

  1. A summary statement of the number of specimens analyzed.
  2. For amplifications and deletions separately, a table representing the results of GISTIC analyses pertaining to that cancer type. The significantly aberrant peak regions of the genome are listed.
  3. Clicking on the chromosome region links displayed on the analyses pages will launch the Integrative Genomics Viewer (IGV) on the data for that region.

More details on available analyses    More details on cancer-centric analyses    Explore data by cancer type now


New User?

Only curators need to register and log in when using the portal. They must request curator privileges in order to manage the data and analyses tools TCGA provides.


Terms of Access   Register


Tutorials / Manuals

Tutorials, analysis descriptions and other documentation is available at:
HELP > DOCUMENTS


News / Events

Feb 4, 2015: Getting IGV to work on Apple Macintosh computers is becoming increasingly difficult as Apple ramps up Java application security. Here is the current work around for OS/X Mavericks.

First, make sure you are getting the IGV launcher file downloaded. It should be in your Downloads folder and be named 'igv.jnlp' or some variant like 'igv-1.jnlp'. If you can find the jnlp file, then you need to allow it to launch IGV in your Java security settings:

(1) Open System Preferences on your Mac.

(2) Select Java (bottom row). The Java Control Panel opens in a separate window.

Select the Security tab, then click on the "Edit Site List..." button to pop up the Exception Site List window.

(3) Click on the Add button in the Exception Site List window.

(4) Under Location, enter https://s3.amazonaws.com, then press the OK button to add the security exception.

(5) Press OK on the Java Control Panel to finalize the security exception.

Now you should be able to go to the Downloads folder and launch IGV with the igv.jnlp file.