How to create plots correlating mRNA expression with PAM50 and my bait protein's expression using cBioPortal database?

Question

[Farah]

Hello,

I am using cBioPortal database to explore more about my proteins of interest. I have read the tutorials that is provided in the cBioPortal website. However, I could not find any information that how I can compare the expression of my proteins's mRNA against PAM50 and its correlation with the expression of my bait protein's mRNA. I am using a breast cancer dataset from cBioPortal database that has both mRNA and protein expression data.

I need to create some plots presenting mRNA expression against PAM50. In other words, how cBioPortal can correlate mRNA expression with PAM50 and my bait protein's expression?

I would highly appreciate your great help and advice.

Best wishes, Farah

[Ram]

I think LinkedOmics has this sort of comparison as a main feature.

Answer 1

[Farah]

Thanks. Actually, from my MS proteomics dataset, after filtering steps, I ended up with 20 proteins, and I used only one bait protein for this pull down experiment. So, I have only a list of 20 proteins (with no quantitate data).

Then, from cBioPortal, I selected a breast cancer dataset from TCGA database that includes mRNA expression data. So, now, for each of these 20 pulled down proteins, I need to create a scatter plot that its x axis displays PAM50 intrinsic subtypes (breast cancer subtypes such as basal-like, luminal A, luminal B, HER2-enriched, normal-like, and claudin-low), and the y axis displays mRNA expression (or z scores or log2 mRNA expression).

This plot correlates mRNA expressions with PAM50 subtypes and also my bait protein's mRNA expression. So, out of these 20 candidate proteins, I can choose those that their mRNA expressions have high correlation with the bait’ mRNA expression, while their expressions are also classified into different breast cancer subtypes (PAM50).

I really appreciate any help regarding how to create such plot.