Question on cBioPortal

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James Reddoch

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Jul 1, 2021, 3:43:55 PMJul 1
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Hi - I am enjoying the database. Of the 314 trials on cBioPortal, which ones have methylation data. I couldn't see a quick way to search for that.
Thanks very much,
Jim

Nikolaus Schultz

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Jul 1, 2021, 3:46:07 PMJul 1
to James Reddoch, cbiop...@googlegroups.com
Hi Jim,

It is only the TCGA studies. I don’t think though that we have the methylation data in the PanCancer Atlas study yet, so at the moment the data are only in the “Firehose Legacy” studies and in some studies that match the TCGA publications.

I hope this is helpful.
Niki.



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Sjoerd van Hagen

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Jul 8, 2021, 6:36:34 AMJul 8
to James Reddoch, cBioPortal for Cancer Genomics Discussion Group, Nikolaus Schultz
Hi Jim,

To add to Niki's reply: a good way to find such studies would be the datasets page: https://www.cbioportal.org/datasets

Using the column button you can add a column for methylation, which can then be used to sort the datasets on the number of samples that have methylation.

There are a few more than just the legacy TCGA ones. The biggest one being Pediatric Acute Myeloid Leukemia (TARGET, 2018).

I hope this helps.

Best,

Sjoerd.

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Sjoerd van Hagen

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James Reddoch

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Jul 8, 2021, 12:12:49 PMJul 8
to Sjoerd van Hagen, cBioPortal for Cancer Genomics Discussion Group, Nikolaus Schultz
Thank you for this information.
A few more questions for one or both of you:
I think for the Firehouse Legacy datasets, "all samples" or "diploid samples" refers to the samples within the given study (i.e. tumor type).  However, for the PanCancer Atlas, is it true that some of the datasets have been normalized across all the studies included in the PanCancer Atlas.  Perhaps it is just the dataset titled "mRNA Expression, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2)" that was normalized in this way, but I am not 100% sure.  From what I understand, the "normal samples" refers to adjacent normal tissue samples within the given tumor type (so not consistent across tumor types, but useful since it is relative to normal tissue and not other tumors).
Which are the mRNA datasets that are normalized against all the studies, and which are the ones normalized within that trial?
We're thinking that if we use data normalized across all the studies, that we will be able to sort for relative high expression of our gene, across tumors.
Thanks very much,
Jim

Jim Reddoch

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Jul 8, 2021, 6:13:12 PMJul 8
to Sjoerd van Hagen, cBioPortal for Cancer Genomics Discussion Group, Nikolaus Schultz
Re-sending to correct typo:

On Jul 8, 2021, at 12:12 PM, James Reddoch <jimre...@gmail.com> wrote:


Thank you for this information.
A few more questions for one or both of you:
I think for the Firehouse Legacy datasets, "all samples" or "diploid samples" refers to the samples within the given study (i.e. tumor type).  However, for the PanCancer Atlas, is it true that some of the datasets have been normalized across all the studies included in the PanCancer Atlas?
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