Closed dhoneyi closed 2 years ago
Hi! Thank you for your interest. That's a good question, we looked at this in some of our previous work (https://www.sciencedirect.com/science/article/pii/S0092867420312538#sec2; see "Paired Measurements Associate Chromatin Peaks and Target Genes in cis") discussing the observed estimated half-lives of enhancer-TSS links to be ~24.4 kb. This was very similar to previous work assessing the effects of enhancers on gene expression using CRISPR perturbation by Gasperini et al (https://www.cell.com/cell/pdf/S0092-8674(18)31554-X.pdf ; see "Distance between Paired Enhancers and Promoters"), where they found it to be ~24 kb as well. Based on these concordant findings, we chose to pad each TSS by +/- 50 kb (so 100 kb around each gene TSS). The further out you go, while you may pick up more correlations, they are more likely to be false positives.
Hope this helps!
Hi,
Thanks for your great work. I wonder why you choose the widow as 50kb but not 100kb or 500kb. Does the window size influence the results?
Thanks!