ArticleBioinformatics (Oxford, England)2018
Quantifying the similarity of topological domains across normal and cancer human cell types.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 40 citations in OpenAlex.
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Building Haplotype-Resolved 3D Genome Maps of Chicken Skeletal Muscle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Article
- DiffDomain enables identification of structurally reorganized topologically associating domains.Nature communications · 2024Article
- Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss.Nature communications · 2023Article
- A Tremendous Reorganization Journey for the 3D Chromatin Structure from Gametes to Embryos.Genes · 2022Review
- Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers.Nature communications · 2022Article
- Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals.BMC biology · 2021Article
- Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory interactions.Nucleic acids research · 2021Article
- Epigenetic landscapes of intracranial aneurysm risk haplotypes implicate enhancer function of endothelial cells and fibroblasts in dysregulated gene expression.BMC medical genomics · 2021Article
- Deciphering hierarchical organization of topologically associated domains through change-point testing.BMC bioinformatics · 2021Article
- A TAD Skeptic: Is 3D Genome Topology Conserved?Trends in genetics : TIG · 2021Review
- Topologically associating domain boundaries that are stable across diverse cell types are evolutionarily constrained and enriched for heritability.American journal of human genetics · 2021Article
- Chromatin Conformation in Development and Disease.Frontiers in cell and developmental biology · 2021Review
- SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering.BMC bioinformatics · 2020Article
- Analysis of the structural variability of topologically associated domains as revealed by Hi-C.NAR genomics and bioinformatics · 2020Article
- Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation.Nucleic acids research · 2020Article
- The 3D Genome as a Target for Anticancer Therapy.Trends in molecular medicine · 2020Review
- The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor.PLoS genetics · 2019Article
- epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology.Bioinformatics (Oxford, England) · 2019Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Motivation: Three-dimensional chromosome structure has been increasingly shown to influence various levels of cellular and genomic functions. Through Hi-C data, which maps contact frequency on chromosomes, it has been found that structural elements termed topologically associating domains (TADs) are involved in many regulatory mechanisms. However, we have little understanding of the level of similarity or variability of chromosome structure across cell types and disease states. In this study, we present a method to quantify resemblance and identify structurally similar regions between any two sets of TADs. Results: We present an analysis of 23 human Hi-C samples representing various tissue types in normal and cancer cell lines. We quantify global and chromosome-level structural similarity, and compare the relative similarity between cancer and non-cancer cells. We find that cancer cells show higher structural variability around commonly mutated pan-cancer genes than normal cells at these same locations. Availability and implementation: Software for the methods and analysis can be found at https://github.com/Kingsford-Group/localtadsim.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.