I'm working with lung cancer data and I'm interested in lncRNAs, I would like to identify lncRNAs that target key pathways.
Recently, I read a paper which discusses about this type of analysis. Here is the paper Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
In this Figure 4A is about lncRNAs that are predicted to target most pathways in MSigDB's Hallmark gene sets, which includes proliferation, immune response, signaling, and DNA damage pathways in multiple tumor types (PAN CANCER)
In the Methods section - Gene set enrichment
They mentioned like this.
When identifying lncRNAs whose targets are enriched in hallmark gene sets,
we estimated gene set enrichment using Fisher’s Exact test between predicted lncRNA targets of each lncRNA and expressed gene set members in each of 14 tumor types using adjusted pFET < 0.01; each test was adjusted for the total number of lncRNAs, lncRNA targets, and gene set tested.
Usually, co-expression network analysis gives us the lncRNAs which fall in the module of protein coding genes and with that we could do pathway analysis. This way we can find which lncRNAs regulate which pathways.
But with the information mentioned in the paper's methods section - how to estimate gene set enrichment using fishers exact test between protein coding genes and lncRNAs?
Can anyone clear my confusion in this? Could you also please tell how this can be done?