Correlation between expressions of two isoforms

Question

[ArseniyBykov]

Dear collegues, I have a list of pairs of gene and its mereged isoform, like TMEFF1 and MSANDT3-TMEFF1, MRPS24 and URGCP-MRPS24. I need to mesure a correlation between expression of merged isoform and expression of downstream(one of two included in merged isoform) gene. I will utilize publically available rna-seq datasbases, however have no ideas how to calculate in these way.

Answer 1

[Satyajeet Khare]

Cufflinks should be able to assemble these isoforms and quantitate them for you. You should be able to plot expression of these isoforms in two different samples using cummeRbund.