Normal tissue mRNA seq source

[Lindsey Mortensen]

Hi there,

Looking to make some expression comparisons using RNAseq data from the HNSCC TCGA PanCan data. It gives me the option to compare Z scores for different genes relative to "normal samples." I've looked into original pubs to uncover any additional information on the normal samples (e.g. sample size, methods, etc.) and what type of tissue these samples are derived from (e.g. any normal tissue or specifically samples from oral mucosa). I am not having a lot of luck and am hopeful you can direct me to a place with some answers? Looked at GDC which has the raw data, but am somewhat unsure how to proceed in finding the specific comparison being made here. Appreciate your help.

Best,

Lindsey

[ole...@thehyve.nl]

Hi Lindsey,

I think the explanation in this documentation page: Z-score normalization script will solve your questions.

Regards,

Oleguer Plantalech-Casals

The Hyve

Op maandag 25 juli 2022 om 07:33:30 UTC+2 schreef lindseymor...@gmail.com:

[Nikolaus Schultz]

Hi Lindsey,

Just to add: The normal samples used by the different TCGA projects are healthy tissue samples from the same organ. I am not sure if details are available on what subset of the organ the sample was from though - I know for ovarian cancer, for example, they used normal Fallopian tubes. The number of samples used also varies from cancer type to cancer type, but from my memory there were 20-30 normal samples per tissue.

I hope this helps.

Niki.

-- 
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/49b0c78d-f918-4b90-8d0d-b32c1a7385f2n%40googlegroups.com.