Pathway Enrichment on lncRNAs

Question

[glady]

Hello everyone,

I'm working on transcriptomic data of human samples, for which I have detected more than 100 expressed lincRNAs. I want to perform a pathway enrichment study on these lncRNAs, How am I supposed to this?

Because, I have the Ensembl Gene_IDs and Gene.Symbols for these lincRNAs, but only 4 lincRNAs of them have Entrez_IDs. And R packages like CusterProfiler will only work on the Entrez_IDs. I want to see in which pathways are these lincRNAs enriched/ playing an important role.

Are there any tools or R packages which can help me in performing GO and GSEA studies on these set of lincRNAs?

Thank you.

Answer 1

[i.sudbery]

You can't.

Pathways in almost all the pathway databases contain descriptions of how proteins work together to perform the biochemical processes of the cell.

But lncRNAs, by their very definition, don't make proteins, so arn't associated with pathways as catalogued in the major pathway databases.