The spatial organization of the genome plays a crucial role in the regulation of gene expression. Recent experimental techniques like HiC have emphasized the segmentation of genomes into interaction compartments that constitute conserved functional domains participating in the maintenance of a proper cell identity. Here, we propose a novel method, IC-Finder, to identify interaction compartments (IC) from experimental Hi-C maps. IC-Finder is based on a hierarchical clustering approach that we adapted to account for the polymeric nature of chromatin. IC-Finder proposes two original options: a probabilistic description of the inferred compartments and the possibility to explore the various hierarchies of chromatin organization. IC-Finder provides a robust and generic tool to uncover the general principles of 3D chromatin folding and their influence on gene regulation.
How to cite: N. Haddad, C. Vaillant & D. Jost (2017) IC-Finder: inferring robustly the hierarchical organization of chromatin folding. Nucleic Acids Research, 45: e81.
IC-Finder.tar.gz: MATLAB/GNU Octave subroutine with userguide
benchmarks.tar.gz: Data for a benchmark of in silico HiC maps
Data used to learn the IC-Finder default parameters are available at: http://membres-timc.imag.fr/Daniel.Jost/DJ-TIMC/Software.html