• Medientyp: E-Artikel
  • Titel: Posterior inference of Hi-C contact frequency through sampling
  • Beteiligte: Zhang, Yanlin; Cameron, Christopher J. F.; Blanchette, Mathieu
  • Erschienen: Frontiers Media SA, 2024
  • Erschienen in: Frontiers in Bioinformatics
  • Sprache: Nicht zu entscheiden
  • DOI: 10.3389/fbinf.2023.1285828
  • ISSN: 2673-7647
  • Schlagwörter: Environmental Engineering
  • Entstehung:
  • Anmerkungen:
  • Beschreibung: <jats:p>Hi-C is one of the most widely used approaches to study three-dimensional genome conformations. Contacts captured by a Hi-C experiment are represented in a contact frequency matrix. Due to the limited sequencing depth and other factors, Hi-C contact frequency matrices are only approximations of the true interaction frequencies and are further reported without any quantification of uncertainty. Hence, downstream analyses based on Hi-C contact maps (e.g., TAD and loop annotation) are themselves point estimations. Here, we present the Hi-C interaction frequency sampler (HiCSampler) that reliably infers the posterior distribution of the interaction frequency for a given Hi-C contact map by exploiting dependencies between neighboring loci. Posterior predictive checks demonstrate that HiCSampler can infer highly predictive chromosomal interaction frequency. Summary statistics calculated by HiCSampler provide a measurement of the uncertainty for Hi-C experiments, and samples inferred by HiCSampler are ready for use by most downstream analysis tools off the shelf and permit uncertainty measurements in these analyses without modifications.</jats:p>
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