Load data from the cBioPortal to GenomeSpace

 

Launch the cBioPortal from GenomeSpace.

  1. Click the cBioPortal icon in the toolbar to launch the cBioPortal.

Download data from cBioPortal and send it to GenomeSpace.


 
 
  1. Locate downloadable data by clicking on the "Download Data" tab in cBioPortal. To download data, change the following parameters:
  2. Select Cancer Study: select from the drop-down menu the study of your choice, e.g. glioblastoma tumor samples.
  3. Select Genomic Profiles: select the datasets that you are interested in, e.g. gene expression data (mRNA expression).
  4. Select Patient/Case Set: select the set of samples you are interested in, e.g. only samples with mRNA expression data.
  5. Enter Gene Set: enter a gene set of interest one of the following ways:
    1. Choose a pre-compiled gene list of interest from the drop-down menu.
    2. Enter a custom gene list of interest in the text box.
  6. Click the Send to GenomeSpace icon.

Save the data to GenomeSpace.

A pop-up window will appear, allowing you to save the compiled dataset to GenomeSpace.


  1. Optional: Choose a specific directory to save the data to, by navigating through the directory tree.
  2. Choose a name for the file, or use the filename automatically generated by the cBioPortal.
  3. Click the Submit button to upload the data to GenomeSpace.