Retrieve TCGA expression data for a single gene
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aush ▴ 40
@aush-9128
Last seen 28 days ago
United States

Is there any way to pull TCGA expression data (in both tumor and matched normals) for one single gene? I want to check it in all TCGA sets (I mean, all tumor types), which makes it very heavy download if I'll have to retrieve whole datasets.
I couldn't find such option in GDCquery(). Also tried to search outside of Bioconductor (cBioPortal for example) with no luck. Any hints?

TCGA TCGAbiolinks • 216 views
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@kevin
Last seen 2 hours ago
Naas, Republic of Ireland

cBioPortal definitely allows you to do this (I have just done it) - please take another look via the Query By Gene --> Download buttons. cBioPortal is not under the scope of Bioconductor though.

For TCGAbiolinks, I am not aware of any way to download data for just a single gene. I would obtain the entire dataset and then filter locally.

Kevin

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thanks for the input Kevin! For cBioPortal - I was confused by the fact that in the "Select Molecular Profiles" field it only has choices "Mutation" and "Copy number alterations", nothing like Expression - though it does provide expression data on the output stage. Unfortunately, cBioPortal doesn't have data on matching normal tissue samples for some reasons.

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Oh yes, I am not sure that cBioPortal has normal data, but please do check again. It's outside the scope of this forum. If not there, then obtaining multiple datasets via TCGAbiolinks will allow you to re-use these time and time again. To give you an idea, I now have most of the TCGA gene expression datasets re-processed from RSEM estimated counts on my hard-disk.

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@tiago-chedraoui-silva-8877
Last seen 9 months ago
Brazil - University of São Paulo/ Los A…

As Kevin said, there is no option to filter by genes in TCGAbiolinks. You would need to download all the data and subset locally.

Here are some codes do download TCGA Raw-counts data:

You can also see the expression of a given gene on GEPIA2: http://gepia2.cancer-pku.cn/, but I don't think you can download the data.

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Obrigado Tiago / Thanks.

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