{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Lou S"],"funding":["National Institute of General Medical Sciences","NIGMS NIH HHS"],"pagination":["e0287521"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC10793909"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["19(1)"],"pubmed_abstract":["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 silico experimental procedure, ChIA-Sim, which imitates the experimental procedures that produce real ChIA-PET, Hi-ChIP, or PLAC-seq data. We show the fidelity of ChIA-Sim to real data by using guiding characteristics of several real datasets to generate data using the simulation procedure. We also used ChIA-Sim data to demonstrate the use of our in silico procedure in benchmarking methods for significant interactions analysis by evaluating four methods for significant interaction calling (SIC). In "],"journal":["PloS one"],"pubmed_title":["An in silico procedure for generating protein-mediated chromatin interaction data and comparison of significant interaction calling methods."],"pmcid":["PMC10793909"],"funding_grant_id":["R01 GM114142","R01GM114142"],"pubmed_authors":["Lin S","Lou S"],"additional_accession":[]},"is_claimable":false,"name":"An in silico procedure for generating protein-mediated chromatin interaction data and comparison of significant interaction calling methods.","description":"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 silico experimental procedure, ChIA-Sim, which imitates the experimental procedures that produce real ChIA-PET, Hi-ChIP, or PLAC-seq data. We show the fidelity of ChIA-Sim to real data by using guiding characteristics of several real datasets to generate data using the simulation procedure. We also used ChIA-Sim data to demonstrate the use of our in silico procedure in benchmarking methods for significant interactions analysis by evaluating four methods for significant interaction calling (SIC). In ","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024","modification":"2026-05-29T11:21:15.757Z","creation":"2025-04-06T12:18:43.395Z"},"accession":"S-EPMC10793909","cross_references":{"pubmed":["38232107"],"doi":["10.1371/journal.pone.0287521"]}}