absolute counts Vs alteration frequency

[Sadaf Abedi]

Hey there,

I am trying to figure out my gene "Fam43a" upregulation or downregulation in various cancer types (TCGA pancancer atlas studies) and in the "cancer type summery'' tab, in the Y-axis when I choose absolute counts, the type of cancers that shows to have highest expressions totally change from the graph with alteration frequency. I am very new to bioinformatic and I do not understand difference of theses 2 words so much.

[JJ Gao]

Hi Sadaf,

Thanks for contacting us.

The z-scores and related concepts are explained here: https://docs.cbioportal.org/user-guide/faq/#what-are-mrna-and-microrna-z-scores

When you query your gene, it will

1. use the zscore cutoff (by default 2) to calculate up/down-regulated (meaning zscores higher/lower than the 2 or -2 by default) for each sample to defined whether a sample is altered in the gene (as you see in OncoPrint)

2. compute the alteration frequency per cancer type. 

3. when you switch to absolute count, the y-axis will be the number of samples instead of frequency.

Note: you might find the Plots tab helpful when investigating gene expression data.

I hope this helps. Please feel free to let us know if you have additional questions.

Best,

-JJ

On Mon, Jun 30, 2025 at 10:23 AM Sadaf Abedi <sadaa...@gmail.com> wrote:

Hey there,

I am trying to figure out my gene "Fam43a" upregulation or downregulation in various cancer types (TCGA pancancer atlas studies) and in the "cancer type summery'' tab, in the Y-axis when I choose absolute counts, the type of cancers that shows to have highest expressions totally change from the graph with alteration frequency. I am very new to bioinformatic and I do not understand difference of theses 2 words so much.

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