To view multiple types of cancer side-by-side, such as ovarian and breast together, you will need to start with a Pan-Cancer dataset and then filter down to just the cancer types you want to see.
There are 2 main Pan-Cancer studies:
TCGA PanCan Study This contains the latest data from the PanCan Atlas project, including many hand curated datasets. It also contains some legacy TCGA data across all cancer types, including GISTIC 2 CNV estimates and miRNAseq estimates.
GDC TCGA PanCan (PANCAN) Study This contains the latest data from the GDC across all cancer types, mapped to hg38
If you do not know which one you wish to use, we recommend starting with the TCGA PanCan Study.
Please see the study specific instructions for which column this is.
Use the filter search bar to search for the cancer type you are interested in. Be sure to type the term as it shows in the phenotype column you added in step 1.
More help can be found at:
Click the Filter + Subgroup menu next to the search bar and select 'Keep Samples'
Click on 'Click on Add column' to the right of the last column to add more data, such as gene expression, to the view.
For the TCGA PanCan (PANCAN), you will want to add the phenotype column:
cancer type abbreviation
For the GDC TCGA PanCan (PANCAN), you will want to add the phenotype column:
Below is an example for viewing breast and ovarian cancer together for the TCGA PanCan Atlas