Genome Biol 2019 Nov 25; 20(1):251
Jackson Laboratory Director's Innovation Fund, HG009409, DK107967, Human Frontier Science Program, Florine Roux Endowment
The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chromatin organization, yet introduce new computational challenges. Thus, we developed MIA-Sig, an algorithmic solution based on signal processing and information theory. We demonstrate its ability to de-noise the multiplex data, assess the statistical significance of chromatin complexes, and identify topological domains and frequent inter-domain contacts. On chromatin immunoprecipitation (ChIP)-enriched data, MIA-Sig can clearly distinguish the protein-associated interactions from the non-specific topological domains. Together, MIA-Sig represents a novel algorithmic framework for multiplex chromatin interaction analysis.
Kim, Minji; Zheng, Meizhen; Tian, Simon Zhongyuan; Lee, Byoungkoo; Chuang, Jeffrey; and Ruan, Yijun, "MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms." (2019). Faculty Research 2019. 246.