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TCGA: Stratify breast cancer cases based on presence of Her2 mutation and get transcription data?
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2.0 years ago
Roman Hillje • 30
Milan, Italy

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?

Thanks!

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19 months ago
TriS ♦ 3.8k
United States, Buffalo

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"

1)

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

2)

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

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

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