So, I have done gene expression analysis using DESeq2. Now, I have several gene which is differentially expressed between normal and cancer sample. I tried to analyze what is the cause of the differentially expressed. I also have data about variation from exome seq with same sample (I got it from NCBI GEO). To find the cause of DE gene, I tried to list all of TF for that gene that I can found from gene card website. My method is really simple, use Pearson correlation too check the correlation coeff and plot it in scatter plot to find the linearity. From this method, I found quite interesting result which is I found 1 TF correlates strongly with downregulation of my target gene (the target gene and TF gene both downregulated). Other TF didn't show this result. I use assay function from DESeq2 object to get the normalized readcount, not the raw count or logarithmic expression level.
My question is, is my method acceptable, both biologically and mathematically?
Also, I found most of the TF and target gene didn't give any strong linear correlation, do I need to calculate it with non-linear correlation method?
Thank you for your suggestion.