Question: Dataset for Breast Cancer with subtypes based on IHC/FISH
gravatar for coolfunkleo
15 months ago by
coolfunkleo0 wrote:

I am looking to download a dataset for breast cancer (microarray or RNA-seq) that has breast cancer classification available from traditional methods such as IHC/FISH to compare with my genetic fingerprint based subtypes. Not looking for those that have PAM50 subtypes. Any recommendations ? Thx

rna-seq • 539 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe45k • written 15 months ago by coolfunkleo0
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe45k
Kevin Blighe45k wrote:


The TCGA has that information (where available) in the clinical information biotab files. Take a look at my answer here in order to give you an idea for breast cancer: A: How to download triple negative breast cancer RNA-seq fpkm data from GDC.

Edit: Following the first part of the short tutorial in my linked thread, I have just downloaded the breast cancer TCGA data and can already see the following data:

  • er_status_by_ihc
  • er_status_ihc_Percent_Positive
  • er_ihc_score
  • pr_status_by_ihc
  • pr_status_ihc_percent_positive
  • pr_positivity_ihc_intensity_score
  • her2_status_by_ihc
  • her2_ihc_percent_positive
  • her2_ihc_score
  • her2_fish_status

To download other data from the TCGA, you can stay on the GDC Legacy Archive and filter the different checkboxes on the left-hand-side in order to select out whatever you need. A lot of data is open access.


METABRIC also profiled by IHC and FISH, I believe, but it is a more 'locked down' dataset and they (from what I understand personally) are careful about the groups to whom they grant access. Take a look:


ADD COMMENTlink modified 15 months ago • written 15 months ago by Kevin Blighe45k
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