queries regarding data sets

[Summer Henderson]

Hi there,

 

We are using data from a few meningioma sets on your site. We had a couple queries regarding the mRNA data:

 

1. Where it is stated ‘relative to diploid’, does this mean that it is compared to a matched normal meninges sample?

 

2. Where the mRNA level is given as N/A does this mean that there has been no mRNA detected or that no mRNA was tested for this sample?

 

I tried to find this out with the user guides, but I could not find the answers.

 

Thank you in advance,
Summer Henderson

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[Benjamin Gross]

Hi Summer,

When we say ‘relative to diploid’, we do not mean matched normal.  We mean expression level is compared to other tumor samples that have diploid copy number.  Regarding N/A values it’s hard to say.  It it could be that the sample wasn’t profiled, but for one reason or another, when the data was curated, the measurement wasn’t provided.  You may be able to find more information if you follow the literature associated with the study.

Best,

Benjamin

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[Summer Henderson]

Thanks Benjamin.

Can you confirm what you mean by ‘other tumor samples that have diploid copy number’?

Summer

[Benjamin Gross]

Hi Summer,

log-transformed z-scores are computed for each sample/gene against the average expression level of the tumor samples in the cohort that are diploid for the gene (no amplifications or deletions)

Best,

Benjamin

[Summer Henderson]

Hi Benjamin,

 

I want to use and reference some data from CC Bioportal from the database called ‘meningioma’. Are you able to help me to identify the publication which this refers to or help me to reference this data?

Thank you,

[Prasanna Jagannathan]

Hi Summer

The study Meningioma  is accessible via the link

https://www.cbioportal.org/study/summary?id=mng_utoronto_2021

On the top of the page, the link to the publication is given.

https://pubmed.ncbi.nlm.nih.gov/34433969/

Please reply only to the cBioPortal group.

thanks

Jag

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[Summer Henderson]

Wonderful, thank you.

Summer

[Summer Henderson]

Benjamin,

I can see my issue now. We are using the version of CBioPortal which requires a login. As you can see from the screenshot, these datasets do not include the publication link.

I am trying to locate this reference now, it is ‘Meningioma from Bayley’

Thank you,
Summer

 

[Benjamin Gross]

Hi Summer,

I don’t see a reference to this dataset in cbioportal.org.   Can you send me the URL to this study from your web browser?

-Benjamin

On Sep 29, 2025, at 10:02 AM, Summer Henderson <summer.h...@plymouth.ac.uk> wrote:

Benjamin, 

I can see my issue now. We are using the version of CBioPortal which requires a login. As you can see from the screenshot, these datasets do not include the publication link.

I am trying to locate this reference now, it is ‘Meningioma from Bayley’

Thank you, 
Summer 

 

<image001.png>

[Summer Henderson]

Sure,

 

It is this:

https://zadehportal2.ccbr.utoronto.ca/study/summary?id=mng_Bayley

[Benjamin Gross]

Hi Summer,

This explains things.  zadehportal2.ccbr.utoronto.ca is not an instance of the cBioPortal that the cbioportal.org open source project maintains or supports.  You’ll have to reach out to the group behind this instance for help accessing this data.

Best,

-Benjamin

[Summer Henderson]

Thank you Benjamin,

Do you know how we find which group it is in order to reach out?