ArticleNucleic acids research2020
Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 24 citations in OpenAlex.
- mosna Reveals Different Types of Cellular Interactions Predictive of Response to Immunotherapies and Survival in Cancer.Molecular & cellular proteomics : MCP · 2026Article
- Analysis of Chromatin Structure Using Network Approaches: A Step-by-Step Guide.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.Nucleic acids research · 2025Article
- Integration of chromosome conformation and gene expression networks reveals regulatory mechanisms in triple negative breast cancer.Frontiers in cell and developmental biology · 2025Article
- Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.bioRxiv : the preprint server for biology · 2024Article
- 3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription.Nature communications · 2023Article
- Esearch3D: propagating gene expression in chromatin networks to illuminate active enhancers.Nucleic acids research · 2023Article
- Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes.Genomics, proteomics & bioinformatics · 2023Article
- Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution.Nature communications · 2023Article
- 3D chromatin connectivity underlies replication origin efficiency in mouse embryonic stem cells.Nucleic acids research · 2022Article
- DAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Understanding 3D genome organization by multidisciplinary methods.Nature reviews. Molecular cell biology · 2021Review
- Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing.International journal of molecular sciences · 2021Article
- Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics.Frontiers in bioinformatics · 2021Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce an R package and a web-based visualization tool for the representation, analysis and integration of epigenomic data in the context of 3D chromatin interaction networks. GARDEN-NET allows for the projection of user-submitted genomic features on pre-loaded chromatin interaction networks, exploiting the functionalities of the ChAseR package to explore the features in combination with chromatin network topology properties. We demonstrate the approach using published epigenomic and chromatin structure datasets in haematopoietic cells, including a collection of gene expression, DNA methylation and histone modifications data in primary healthy myeloid cells from hundreds of individuals. These datasets allow us to test the robustness of chromatin assortativity, which highlights which epigenomic features, alone or in combination, are more strongly associated with 3D genome architecture. We find evidence for genomic regions with specific histone modifications, DNA methylation, and gene expression levels to be forming preferential contacts in 3D nuclear space, to a different extent depending on the cell type and lineage. Finally, we examine replication timing data and find it to be the genomic feature most strongly associated with overall 3D chromatin organization at multiple scales, consistent with previous results from the literature.
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