As a part of a project I tried to find out if there is any interaction between a list of mRNAs and a list of lncRNAs.
The list of my lncRNAs has been obtained from a microarray platform (GSE58828).
In this platform like other lncRNA platforms, the names of lncRNAs is some thing like: ASHG19A3A045113.
Moreover I have only the sequence of the 60nt probes used in microarray.
My first question is: How can I get the gene symbol for my lncRNAs from their IDs?
and is it possible that I check the interaction of these 60nt probes with my mRNAs instead of total length of lncRNAs?
If yes, what cutoff should I apply on "normalized detaG"? is <= -0.2 is reasonable?
I will appreciate any help in advance