Document Type

Article

Publication Date

11-25-2019

Keywords

JGM

JAX Source

Genome Biol 2019 Nov 25; 20(1):251

PMID

31767038

DOI

https://doi.org/10.1186/s13059-019-1868-z

Grant

Jackson Laboratory Director's Innovation Fund, HG009409, DK107967, Human Frontier Science Program, Florine Roux Endowment

Abstract

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.

Comments

This open access article is licensed under a Creative Commons Attribution 4.0 International License

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