mRNA Expression: z-score to diploid or all samples?

[Ashwin Nandakumar]

Dear cbioportal team, 

I am planning on comparing the genes expressed when AR gene expression is high (AR: EXP>1) vs low (AR: EXP<-1). To do this, I need to select a method of comparing mRNA expression: z-score to diploid samples or all samples. What do you think is the most appropriate method to choose? I'm just a bit confused about what both of these mean. 

Thanks so much for your help! 

Best wishes,

Ashwin

Ashwin Menon Nandakumar
DPhil student, Department of Oncology
Student Representative, Department of Oncology

University of Oxford
+44 7517 295306

[Tali Mazor]

Hi Ashwin,

Both of these are z-score profiles, which means they indicate the number of standard deviations from the mean of expression of the same gene in a reference population. These profiles differ in their definition of the reference population: all tumor samples in the study vs only those tumor samples that are diploid (no copy-number change) for the gene in question. We recommend using the z-scores relative to all samples.

Note that your results will change slightly depending on which profile you use, but the ranking of samples by expression will remain the same.

-Tali

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[M B]

Hi Ashwin,

I got different survival curves results with both of them, do you have any experience with that?

Kind regards,

Mohamed.

Mohamed Wahba | PhD Candidate 

 

THE UNIVERSITY OF SYDNEY
N411, Pharmacy and Bank Building A15 | The University of Sydney | NSW | 2006 
T +61 2 9351 7045 | M +61404783239 
E mwah...@uni.sydney.edu.au

[M B]

Hi Tali,

I tried both, my results in terms of survival is completely different with both of them. Any clue?

Kind regards,

Mohamed.

Mohamed Wahba | PhD Candidate 

 

THE UNIVERSITY OF SYDNEY
N411, Pharmacy and Bank Building A15 | The University of Sydney | NSW | 2006 
T +61 2 9351 7045 | M +61404783239 
E mwah...@uni.sydney.edu.au