RT Journal
A1 Djekidel, Mohamed Nadhir
A1 Chen, Yang
A1 Zhang, Michael Q.
T1 FIND: difFerential chromatin INteractions Detection using a spatial Poisson process
JF Genome Research 
JO Genome Research 
YR 2018 
FD March 01 
VO 28 
IS 3 
SP 412 
OP 422 
DO 10.1101/gr.212241.116 
UL http://genome.cshlp.org/content/28/3/412.abstract 
AB Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio.