LncRNA and Immune-related genes

Question

[jonathanpa12]

Hello everyone

I got a list of up-regulated and down-regulated LncRNAs and Immune-related genes from a differential analysis of a RNAseq. I would like to know whether any of the LncRNAs participate in the regulation of expression or function of those immune-related genes, but I don´t know if it´s possible to infer it in silico. Is there any tool that could explore?

Thank you so much.

[igor]

Maybe this helps: non-coding RNAs target predictions

[Kevin Blighe]

Can you elaborate on what you mean by "immune-related" genes?, i.e., how you defined them and give a few examples? Your task may be as simple as regressing each lincRNA to each immune-related gene, and taking it from there with statistically significant associations.

Answer 1

[Antonio R. Franco]

There is not a clear and useful method to do what you want. LncRNA are not conserved, and you cannot follow the rules of orthologous genes as in protein-coding genes

You have a choice, though. Some lncRNA are present in the UTR of the genes that regulates. So you can give a try by using Bedtools and find those lncRNA located close to these regions and in both orientations if your cDNA library is stranded

But for sure, this is only a short part of the story..