Question: Download TCGA cancer and normal tissue gene expression data from GDC
gravatar for Nicolas Rosewick
3.3 years ago by
Belgium, Brussels
Nicolas Rosewick8.5k wrote:


SInce TCGA data are now on NCI website how can I download gene expression data (FPKM) for breast cancer and associated normal tissue. I do not find any "normal tissue" option (maybe I missed it..).

For example here's the selection for breast cancer expression data :{%22op%22:%22and%22,%22content%22:[{%22op%22:%22in%22,%22content%22:{%22field%22:%22cases.project.primary_site%22,%22value%22:[%22Breast%22]}},{%22op%22:%22in%22,%22content%22:{%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]}},{%22op%22:%22in%22,%22content%22:{%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22HTSeq%20-%20FPKM%22]}}]}

FYI I'm just interested in FPKM from several genes (~50) but I had to download the whole expression file. Is that right or is there an easiest way to have directly the FPKM for my subset of genes of interest ?


cancer gdc tcga normal • 2.8k views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Nicolas Rosewick8.5k

On the data search you can select "Add cases filter", and then select sample_type. You can now add "Solid tissue dervied normal" as a filter. However, there are far fewer normal than tumor samples.

ADD REPLYlink written 3.3 years ago by i.sudbery6.3k
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