How can we generate super-enhancer mediated lncRNA network to detect prognostic biomarkers in cancer via indication of upregulated / downregulated gene states....
I think lncRNA itself could be used as biomarker, which would be more sensitive than its downstream gene. The field is promising but not very elusive till now as super-enhancer loop is dynamic rather than more conserved TAD region. I'm not very familiar with the field, but I try to guess :)
in specific cell type with two status (with or without treatment, from healthy or disease tissue)
1. you identify super enhancer with H3K27ac or Key transcription factor ChIP-seq data.
2. identify IncRNA with aligned RNA-seq data.
3. compare super-enhancer region between different cell status or disease status with gene expression data
4. identify the lncRNA located in the changing SE region.
5. test the LncRNA with the gene expression data in interference experiment that disfunction the lncRNA.
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