ArticleNucleic acids research2012
On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Analysis of chromatin structure reveals the connection between sQTLs and the splicing of distant genes.Scientific reports · 2025Article
- Assessing chromatin relocalization in 3D using the patient rule induction method.Biostatistics (Oxford, England) · 2023Article
- Can 3D diploid genome reconstruction from unphased Hi-C data be salvaged?NAR genomics and bioinformatics · 2022Article
- Comparative 3D genome architecture in vertebrates.BMC biology · 2022Article
- Principal curve approaches for inferring 3D chromatin architecture.Biostatistics (Oxford, England) · 2022Article
- Assessing stationary distributions derived from chromatin contact maps.BMC bioinformatics · 2020Article
- The Functional 3D Organization of Unicellular Genomes.Scientific reports · 2019Article
- Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.Nature communications · 2019Article
- Comparative 3D genome organization in apicomplexan parasites.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Improved accuracy assessment for 3D genome reconstructions.BMC bioinformatics · 2018Article
- Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages.Nature communications · 2018Article
- Heterogeneous Spatial Distribution of Transcriptional Activity in Budding Yeast Nuclei.Biophysical journal · 2017Article
- A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions.Genome biology · 2016Article
- 4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?Genome biology · 2016Review
- Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Discovering hotspots in functional genomic data superposed on 3D chromatin configuration reconstructions.Nucleic acids research · 2016Article
- The 3D folding of metazoan genomes correlates with the association of similar repetitive elements.Nucleic acids research · 2016Article
- Genome-wide replication landscape of Candida glabrata.BMC biology · 2015Article
- Analysis methods for studying the 3D architecture of the genome.Genome biology · 2015Review
- Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints.PLoS computational biology · 2015Article
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2 authors.
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Abstract
A growing body of experimental evidence supports the hypothesis that the 3D structure of chromatin in the nucleus is closely linked to important functional processes, including DNA replication and gene regulation. In support of this hypothesis, several research groups have examined sets of functionally associated genomic loci, with the aim of determining whether those loci are statistically significantly colocalized. This work presents a critical assessment of two previously reported analyses, both of which used genome-wide DNA-DNA interaction data from the yeast Saccharomyces cerevisiae, and both of which rely upon a simple notion of the statistical significance of colocalization. We show that these previous analyses rely upon a faulty assumption, and we propose a correct non-parametric resampling approach to the same problem. Applying this approach to the same data set does not support the hypothesis that transcriptionally coregulated genes tend to colocalize, but strongly supports the colocalization of centromeres, and provides some evidence of colocalization of origins of early DNA replication, chromosomal breakpoints and transfer RNAs.
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