Question about mRNA expression (log2) plot the TCGA

[Julius Reckmann]

Hey. I´m doing research on CD87 as a potential target for immunotherapy, especially in AML. CD87´s gene is PLAUR. The path I follow to view expression data is this: TCGA PanCancer Atlas Studies-Query by gene- mRNA expression checked (whichever of the three listed options doesn’t matter concerning how the Plot ends up looking) -clinical attribute - cancer type detailed- Acute myeloid leukemia- mRNA- mRNA Expression,RSEM-

I now end up with the attached Plot. It shows a box plot with a (log2) median of 9. This means that the median PLAUR RNA expression im AML  is 2 to the ninth power times increased. But compared to what now? The mRNA expression (in what, AML Blasts??) is two to the ninth power increased compared to healthy people (´s myeloid cells?) ? What cells were sequenced ? Most importantly, the 2^9 relative increase of the gene in AML is 2^9 times increased compared to what? The 2^0 would be consistant with healthy people or what? I don’t know what the baseline to this increase is.

Thanks if anyone answers this email. Would be greatly appreciated. 

[Nikolaus Schultz]

Hi Julius,

The log2 numbers are not fold changes - they are log values of the RSEM-adjusted read counts, so basically an estimate of the overall expression of the gene in a given sample. There are no normal or reference samples used to determine these read counts.

Niki.

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