Methylation - mRNA expression (RNA Seq V2 RSEM) (log2) plot

[Eleonora]

Good evening,

I am not still really confident with cBioportal, I would ask some explanations about the Methylation - mRNA expression (RNA Seq V2 RSEM) (log2) plot.

I am trying to build it with the gene GSPT1 but it is a general question about how this plot is built.

1) In the query, I selected the dataset ' TCGA,Provisional ', in order to retrieve and view the plotted data. I was able to download the methylation data but I didn't find the mRNA expression (RNA Seq V2 RSEM) data, I looked for them in the new TCGA website but I didn't found them. 

Where could I find them? Where are they available?

2) In the case of the gene GSPT1, having a look to methylation data, the plotted value for each sample corresponds to the probe cg15834294. Is it related to the following explanation that I found in the FAQs: "For genes with multiple probes, we only include methylation data from the probe with the strongest negative correlation between the methylation signal and the gene's expression."?

Thanks very much for your attention,

Sincerely

Eleonora

[JianJiong Gao]

Hi Eleonora,

1) You can download the data with the Download Data query form (next
to Query in the home page) or in the Utilities section in the Plots
tab.

2) Yes.

Best,
-JJ

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[Eleonora]

Thank you for your reply, it was helpful.

I have another question: the reported value of mRNA expression is referred to the gene expression, while, the beta value is chosen evaluating the correlation with the mRNA expression of the correspondent probe. 

I would like to retrive the data of the value of expression of the single probe. Are they available on the TCGA or cBioportal too? Is there a way to retrive them?

[JianJiong Gao]

Hi,

You can get the data from Broad Firehose: http://gdac.broadinstitute.org/

Best,
-JJ