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.

基于聚合物的模拟和实验研究表明，参与染色质环形成的相邻 DNA 纤维之间存在空间依赖性。然而，检测差异染色质相互作用的现有策略假设相互作用的片段在空间上独立于附近的其他片段。为了解决这个问题，我们开发了一种新的计算方法 FIND，它考虑了相互作用位点之间的局部空间依赖性。 FIND 使用空间泊松过程来检测差异染色质相互作用，这些相互作用显示出它们的相互作用频率与其邻居的相互作用频率存在显着差异。仿真和生物数据分析表明，FIND 优于广泛使用的基于计数的方法，并且具有更好的信噪比。