Identifying common genes which show different transcript and protein expression

Question

[vin23]

Hello all, I am working on a project with includes working with R. I am performing an analysis with gene and protein datasets. I want to identify common genes between 2 samples (two types of cells) and are having different expression patterns, which means I need to identify genes which shows up regulation in gene expression and down regulation in protein expression. I have tried taking ratio of gene and protein and applied statistical tests to identify the differential genes but I was unsuccessful. So can you suggest any tests or method by which I can identify the genes.

Answer 1

[ATpoint]

Do DEG and DEP separately, and then simply select genes that are significantly up in DEGs and down in DEPs, or vice versa. I do not think that there is a direct test for this as these are completely different types of experiments.

[vin23]

Thank you so much