Question: TCGA: Stratify breast cancer cases based on presence of Her2 mutation and get transcription data?
gravatar for Roman Hillje
3.1 years ago by
Roman Hillje40
Milan, Italy
Roman Hillje40 wrote:

Hey guys,

I have a slightly frustrating problem that should not take more than a couple of minutes to solve, but anyway I don't seem to be able to do it... I'd like to access TCGA data, specifically expression/transcription (RNAseq or microarray) in breast cancer, however distinguished by the presence of Her2 mutation. I was assured by a colleague that Her2 mutation is one of the first things to be tested when diagnosed with breast cancer as it has major implications for the choice of therapy, so the data should be available somehow. Can anybody help me out?


rna-seq tcga api • 1.1k views
ADD COMMENTlink modified 3.1 years ago by TriS4.2k • written 3.1 years ago by Roman Hillje40
gravatar for TriS
3.1 years ago by
United States, Buffalo
TriS4.2k wrote:

simplest ways:

go to cBioportal --> select your tumor type --> click on the right inside the link for "summary" --> on the top click the "download data"


from here open the mutation data, skim for Her2 and get the corresponding patient IDs

then open the RNASeq data and select out the list of patients you just saved


open the clinical data file and check for the presence of annotation for Her2 mutation (it might be there)

then you do the same as above, save the patients ID and use them to extract RNASeq data

ADD COMMENTlink written 3.1 years ago by TriS4.2k

Wow, you are a hero! Thanks so much, this was exactly what I was looking for!

ADD REPLYlink written 3.1 years ago by Roman Hillje40
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