Entering edit mode
17 days ago
Apollonia
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0
Hi all,
I am working on cancer subtyping and saw trancriptional subtype labels for TCGA-GBM patients on cBioPortal.
I know that the subtying of Verhaak (2010) is outdated and glioblastoma genexp subtyping is still an ongoing discussion.
So, when I couldn't find these subtyping labels on GDC data portal, I thought they just removed it. But now I still can find those labels on XenaBrowser and cBioPortal.
Do you have any insight on this? Would it be still valid to use these labels?
Thanks in advance.
TCGA-GDC-portal is the main repository. Other portals may provide alternate views/analyses of the data. If you no longer find things on GDC portal then you should email GDC help desk and ask before using the labels.
I am not sure what you meant by saying "subtype labels". GDC does not carry these "labels" in the data portal. These labels came from research analysis and published in peer-reviewed papers, and the only place you might find them in the GDC should be in the publication pages.
On the other hands, if you are talking about the raw gene expression data that were used to generate these labels, GDC used to have them in the legacy archive. GDC had communicated in different channels, including user mail list, for almost a year that these legacy data would be removed with the retirement of legacy archive. It seems that TCGA-GBM is somewhat special that a significant amount of cases only have U133 expression array, but not have RNA-Seq. As many users are asking about these files, the GDC will bring this subset of raw array data back (probably in the next data release). I hope this is what you are looking for. Btw, I believe DCF still have these data and they can be accessed via cloud resources (Terra, 7-bridges, etc).