comparison of gene expression across different datasets

[Pal, Sharmistha]

Good morning

First, thank you to the team for cBioPortal.

 

I have a specific question. I want to compare the expression of say “gene X” in Diifuse midline glioma patients profiled in OPEN PBTA cohort to that in GBM samples profiled in TCGA. Both datasets are RNA-seq

 

Can I just extract the z-scores of both datasets and compare gene “X” expression in DMG vs GBM?

 

Sharmistha

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[Nikolaus Schultz]

Hi,

Can you please clarify exactly which cohorts you are trying to compare? I can’t seem to find the “Open PBTA” cohort you are referring to.

The z-scores for each gene and sample will tell you the relative expression of that gene compared to all other samples in the cohort. So a comparison between samples in different studies will not work when using z-scores. Within the TCGA cohorts, you can, however, compare expression levels (not z-scored) between different studies.

I hope this is helpful.

Niki.

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[Pal, Sharmistha]

Thanks Niki

I was refering to  the datasets below:

1. Open Pediatric Brain Tumor Atlas (OPENPBTA) and
2. Glioblastoma (TCGA Cell 2013)

 

Sharmistha

 

From: Nikolaus Schultz <nsch...@gmail.com>
Date: Friday, April 29, 2022 at 2:10 PM
To: Pal, Sharmistha <Sharmis...@DFCI.HARVARD.EDU>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] comparison of gene expression across different datasets

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[Nikolaus Schultz]

I see - I don’t see that study in the public cBioPortal at cbioportal.org.

But regardless, what I said about comparing z-scores between studies still applies.

Niki.