I have downloaded ENCODE chip-seq peaks for HepG2 cell line with FOXA2(TF). I found this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794179/#!po=21.4286 i took the chip-seq data for HepG2 in FOXA2 they have in this paper I used venn diagramm to find the overlapping peaks and for my suprise the overlapping peaks weren so much as i expected, could this happen. I expected one cycle inside the other in biggest percentage
I don't know about this TF and cell line, but 10% overlap [438 / (1297 + 438 + 2476)] doesn't surprise me much really, it's small but still not unusual, especially since the data come from different labs (right?).
Also, looking at overlap by number of peaks can be misleading since you give equal weight to all peaks, even those that are at the boundary of significance and might be gained or lost depending on sequencing depth, peak calling sensitivity etc.
(I'm still looking for a good way to assess consistency of peaks between two or preferably more replicates)
According to the screenshot, you are using Venny. Venny is used for overlapping discrete values. This is good for things like genes that have specific names. Peaks are usually identified by genomic coordinates and they span regions of different size. If you overlap ranges with Venny, you will not get an overlap unless the regions are identical. If the two peaks are off by even 1 base, Venny will not consider them overlapping.