Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure [article]

Abbas Roayaei Ardakany, Ferhat Ay, Stefano Lonardi
2019 bioRxiv   pre-print
Motivation:High-throughput conformation capture experiments such as Hi-C provide genome-widemaps of chromatin interactions, enabling life scientists to investigate the role of the three-dimensionalstructure of genomes in gene regulation and other essential cellular functions. A fundamental problem inthe analysis of Hi-C data is how to compare two contact maps derived from Hi-C experiments. Detecting similarities and differences between contact maps is critical in evaluating the reproducibility
more » ... f replicate experiments and identifying differential genomic regions with biological significance. Due to the complexity of chromatin conformations and the presence of technology-driven and sequence-specific biases, the comparative analysis of Hi-C data is analytically and computationally challenging.Results:We present a novel method called Selfish for the comparative analysis of Hi-C data that takes advantage of the structural self-similarity in contact maps. We define a novel self-similarity measure to design algorithms for (i) measuring reproducibility for Hi-C replicate experiments and (ii) finding differential chromatin interactions between two contact maps. Extensive experimental results on simulated and real data show that Selfish is more accurate and robust than state-of-the-art methods.
doi:10.1101/540708 fatcat:hbmcrt2phzb5ne3ynrzy2uig6m