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Loopsim: Enrichment Analysis ofChromosomeConformation Capture with Fast EmpiricalDistribution Simulation

ABSTRACT: The three-dimensional organization of the genome intricately influences the regulation of genes.In particular, chromatin can exist as loop structures that enable long-range regulatory interactions. By utilizingchromosome conformation capture techniques such as Hi-C, valuable information regarding the organizationof these loop structures in 3D space can be obtained. While gene-set enrichment has become a standard down-stream analysis for different genomic data to provide biological context, tools that providefunctionalenrich-ment for high throughput assays capturing chromosome conformation are relatively limited. Here, we presentLoopsim, 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 approachthat considers loop size, intervals, loop-loop distances, and structure;itthencomputes statistics based on theempirical null distribution.

ORGANISM(S): Homo sapiens

PROVIDER: GSE279870 | GEO | 2025/07/23

REPOSITORIES: GEO

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