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bioRxiv · 10.1101/2024.06.03.595407

Loopsim: Enrichment Analysis of ChromosomeConformation Capture with Fast EmpiricalDistribution Simulation

Shaked, G.·Zhang, H.·Zhang, Z.·Gudjonsson, J. E.·Elder, J. T.·Patrick, M. T.·Tsoi, L. C.
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Abstract

SummaryGene regulation is intricately influenced by the three-dimensional organization of the genome. In particular, chromatin can exist in loop structures that enable long-range regulatory interactions. By utilizing chromosome conformation capture techniques such as Hi-C, valuable information regarding the organization of these loop structures in 3D space can be obtained. While functional/feature enrichment has become a standard downstream analysis for different genomic data to provide biological context, tools that developed specifically for high throughput assays capturing chromosome conformation are relatively limited. Here, we present Loopsim, a command-line application that performs enrichment analysis on Hi-C loop profiles against user-defined regions. Loopsim efficiently simulates a background distribution using a distinctive sampling approach that considers loop size, intervals, loop-loop distances, and structure; it then computes loop-level statistics based on the empirical null distribution. AvailabilityLoopsim is a Python package available via PyPI (https://pypi.org/project/loopsim) and the source code is available on GitHub (https://github.com/CutaneousBioinf/Loopsim) under the MIT license.

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Shaked, G., Zhang, H., Zhang, Z., Gudjonsson, J. E., Elder, J. T., Patrick, M. T., Tsoi, L. C.. 2024-06-04. Loopsim: Enrichment Analysis of ChromosomeConformation Capture with Fast EmpiricalDistribution Simulation. https://doi.org/10.1101/2024.06.03.595407

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