ArticleNucleic acids research2013
Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Three-dimensional genome organization via triplex-forming RNAs.Nature structural & molecular biology · 2021Article
- The Functional 3D Organization of Unicellular Genomes.Scientific reports · 2019Article
- Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.Nature communications · 2018Article
- A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps.Bioinformatics (Oxford, England) · 2016Article
- Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation.PLoS computational biology · 2016Article
- 4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?Genome biology · 2016Review
- Quantification of DNA cleavage specificity in Hi-C experiments.Nucleic acids research · 2016Article
- Analysis methods for studying the 3D architecture of the genome.Genome biology · 2015Review
- Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.PLoS computational biology · 2015Article
- 3D hotspots of recurrent retroviral insertions reveal long-range interactions with cancer genes.Nature communications · 2015Article
- Distance-based assessment of the localization of functional annotations in 3D genome reconstructions.BMC genomics · 2014Article
- A statistical model of ChIA-PET data for accurate detection of chromatin 3D interactions.Nucleic acids research · 2014Article
- Reproducibility of 3D chromatin configuration reconstructions.Biostatistics (Oxford, England) · 2014Article
- HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization.Bioinformatics (Oxford, England) · 2014Article
- Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts.Genome research · 2014Article
- The Genomic HyperBrowser: an analysis web server for genome-scale data.Nucleic acids research · 2013Article
- Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data.Quantitative biology (Beijing, China) · 2013Article
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7 authors.
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Abstract
The study of chromatin 3D structure has recently gained much focus owing to novel techniques for detecting genome-wide chromatin contacts using next-generation sequencing. A deeper understanding of the architecture of the DNA inside the nucleus is crucial for gaining insight into fundamental processes such as transcriptional regulation, genome dynamics and genome stability. Chromatin conformation capture-based methods, such as Hi-C and ChIA-PET, are now paving the way for routine genome-wide studies of chromatin 3D structure in a range of organisms and tissues. However, appropriate methods for analyzing such data are lacking. Here, we propose a hypothesis test and an enrichment score of 3D co-localization of genomic elements that handles intra- or interchromosomal interactions, both separately and jointly, and that adjusts for biases caused by structural dependencies in the 3D data. We show that maintaining structural properties during resampling is essential to obtain valid estimation of P-values. We apply the method on chromatin states and a set of mutated regions in leukemia cells, and find significant co-localization of these elements, with varying enrichment scores, supporting the role of chromatin 3D structure in shaping the landscape of somatic mutations in cancer.
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