An in silico procedure for generating protein-mediated chromatin interaction data and comparison of significant interaction calling methods

• Published in: PloS one Vol. 19; no. 1; p. e0287521
• Main Authors: Lou, Shuyuan, Lin, Shili
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17.01.2024; Public Library of Science (PLoS)
• Subjects: Accuracy; Analysis; Benchmarks; Binding sites; Biology and life sciences; Chromatin; Chromatin Immunoprecipitation Sequencing; Chromosomes; Comparative analysis; Computer and Information Sciences; Computer Simulation; Datasets; DNA; Enzymes; Genomes; Methods; Proteins; Research and Analysis Methods; Sequence Analysis, DNA - methods; Signal to noise ratio; Simulation; Transcription factors; United States

The ability to simulate high-throughput data with high fidelity to real experimental data is fundamental for benchmarking methods used to detect true long-range chromatin interactions mediated by a specific protein. Yet, such tools are not currently available. To fill this gap, we develop an in sili...