FIND: DifFerential Chromatin INteractions Detection Using a Spatial Poisson Process



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Cold Spring Harbor Lab Press, Publications Dept


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.


Includes supplementary material


Human genome, Bioconductor (Computer file), Gene expression, Chromatin, Poisson processes

National Basic Research Program of China (2017YFA0505503), the National Natural Science Foundation of China (91729301, 31671384, 31301044, and 81630103).


CC BY-NC 4.0 (Attribution-NonCommercial), ©2018 The Authors