Published statistics about genome biology¶
Summary¶
These statistics aim to provide a reference for your cutoffs.
average distance between enhancer and target genes¶
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1924-8
95th percentile distance from all positive cCRE-gene pairs
These distance cutoffs ranged from 120 kb (RNAPII ChIA-PET in HeLa) to 1.83 Mb (Hi-C in K562).
`
the median genomic distances of the positive pairs are 46,934 bp in K562 and 37,556 bp in MCF-7
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007436
`
`
and ~91% of loop anchors were associated with
either a promoter or an enhancer29, as expected, with a median distance of 130 kb
https://marsonlab.ucsf.edu/sites/marsonlab.ucsf.edu/files/wysiwyg/nihms936848.pdf
`
``` However, the distance between a target gene and its regulatory elements can be as far as 2 or 3 Mb (Krivega and Dean 2012)
For the MCF7 and Hippo data, the average distances between a target gene and its farthest enhancer were 246 and 99 kb, respectively
https://www.genetics.org/content/genetics/209/3/699.full.pdf ```
``` The median distance between loop anchor midpoints was 255 kb, and nearly 10% were over 1 Mb in size (Supplementary Fig. 2b). This established a map of chromatin loops in human pancreatic islets https://escholarship.org/content/qt9mf3h56q/qt9mf3h56q_noSplash_d10cf424c9c11237b1723be14e064c73.pdf