Query regarding the units of expression on Y-axis.

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Rahul Sanawar

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Nov 21, 2022, 2:16:05 PM11/21/22
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Hi cBioportal,

I am a Postdoc researcher from Albert Einstein College of Medicine, New York. I have used cBioportal tool to analyze the correlation of one gene and a protein (Notch1) among cohorts separated based on P53 mutation. I have taken out the expression values from the datasets used below and made graphs. I am planning to put these two graphs in my paper.

But I have a query regarding these two graphs. I DO NOT know the units of the expression values and hence cannot use these graphs in my paper without showing the units of expression values on the Y-axis. 
The first graphs show the mRNA expression, and the second graph shows the protein expression. 
Could you please help me in providing the units for both of these graphs? It would be a great help. 
Your early reply would be very much appreciated. Thanks
 


Warm Regards,
Rahul Sanawar

Tali Mazor

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Nov 22, 2022, 3:01:52 PM11/22/22
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Hi Rahul,

For the mRNA data in the METABRIC study, the value is log intensity levels. You can see this in the website by hovering over the (i) icon (screenshot below) or in the metadata file if you pulled the data directly from the datahub (https://github.com/cBioPortal/datahub/blob/master/public/brca_metabric/meta_mrna_agilent_microarray.txt)

image.png

For the RPPA data in the firehose legacy study, the description in the portal is: "Protein expression measured by reverse-phase protein array"
I've cc'ed our head curator to see if she can provide any additional information.

-Tali





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Rahul Sanawar

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Nov 22, 2022, 4:40:43 PM11/22/22
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Thank you for your response. I got it now.


Warm Regards,
Rahul Sanawar

From: Tali Mazor <tma...@ds.dfci.harvard.edu>
Sent: Tuesday, November 22, 2022 3:01 PM
To: Rahul Sanawar <rahul....@einsteinmed.edu>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>; ritika...@gmail.com <ritika...@gmail.com>
Subject: Re: [cbioportal] Query regarding the units of expression on Y-axis.
 
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Rahul Sanawar

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Nov 23, 2022, 3:18:09 PM11/23/22
to Tali Mazor, cbiop...@googlegroups.com, ritika...@gmail.com
Hi Tali,

I could not get the answer from the reply. I tried to click on the link you shared for mRNA expression, but I am not able to figure out whether what is the meaning of log intensity on the hover information- Does that signify log2 or Log10? 

Also, for the protein graph, I understand that the description says, "Protein expression measured by reverse-phase protein array" and I had already shown that on my Y-axis, but I am looking for the actual unit of the protein expression measured on Y-axis. Please let me know. 


Warm Regards,
Rahul Sanawar

From: Tali Mazor <tma...@ds.dfci.harvard.edu>
Sent: Tuesday, November 22, 2022 3:01 PM
To: Rahul Sanawar <rahul....@einsteinmed.edu>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>; ritika...@gmail.com <ritika...@gmail.com>
Subject: Re: [cbioportal] Query regarding the units of expression on Y-axis.
 
CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails.
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