I already know the pathway but want to know the upstream lncRNAs that regulates that pathway using the datasets and bioinformatics.
Sankalp Sharma I know the pathway unregulated in the particular condition and I'm interested to know which lncRNAs regulate this pathway instead of the conventional way in which we start with the lncRNAs and find the target gene or the pathway. In short, I have to go in the reverse way.
I think you can do correlation analysis between lncRNA expression, For each gene within the pathway, calculate the correlation coefficients between its expression and the expression of all known lncRNAs (list can be obtained from LNCipedia etc). then using the approriate threshold can narrowdown the list.
or the other method,
As we know the pathway then get the gene list for that pathways and can Search for lncRNAs that are located near the genes in the pathway and may act as cis-regulatory elements/ trans by using tools that predict the potential of lncRNAs to act as trans-regulatory elements by interacting with genes at the transcriptional or post-transcriptional level like LncTar (https://www.cuilab.cn/lnctar)
hope that helps
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Molecular Methods
- Cloning