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decode protein-lncRNA, protein-ncRNA, protein-mRNA interactions from CLIP-Seq data yjhua2110 RNA Sequencing 9 06-04-2015 12:12 AM

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Old 07-02-2019, 07:07 AM   #1
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Default How to create plots correlating mRNA expression with PAM50 and my bait protein's expr


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 baití 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.
Many thanks.
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cbioportal, correlation coefficient, mrna expression, pam50, rna-seq

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