How to study the co-expression of lncRNA with mRNA

[mayankkaashyap]

Hi,
I am a PhD student and working on lncRNA from a plant genotype. May I please request if there is an easy way (although nothing comes easy) to study the co-expression of lncRNA (long non-coding RNA) with mRNA in order to predict their role in regulating the coding genes. There are easy database like Co lncRNA but they have human database. Got to know WGCNA package in R but that seems to be too difficult for me. I have FPKM values for both the RNA. Please add to my understanding.
Thanks.

[hideandSEQ]

Your best bet is probably gonna be conducting knockdown or knockout experiments and observing changes in expression or histone modifications. Transfection to overexpress may be helpful too.

This will absolutely not be an easy task. Even with the most intensely studied human lncRNAs (Xist, Malat-1), there seems to be gaps in our understanding of how and what they interact with.

[mayankkaashyap]

Thanks, hideandSEQ for your reply. This is really a good idea.