ArticlePLoS computational biology2015
Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 51 citations in OpenAlex.
- Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks.Genome research · 2025Article
- Chromatin remodeler Activity-Dependent Neuroprotective Protein (ADNP) contributes to syndromic autism.Clinical epigenetics · 2023Review
- A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships.Genome biology · 2022Article
- Prediction of gene co-expression from chromatin contacts with graph attention network.Bioinformatics (Oxford, England) · 2022Article
- Chromatin Hubs: A biological and computational outlook.Computational and structural biotechnology journal · 2022Review
- Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics.Frontiers in bioinformatics · 2021Article
- A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons.Genome medicine · 2020Article
- Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization.Nucleic acids research · 2019Article
- A subset of topologically associating domains fold into mesoscale core-periphery networks.Scientific reports · 2019Article
- Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates.PLoS genetics · 2019Article
- ChiCMaxima: a robust and simple pipeline for detection and visualization of chromatin looping in Capture Hi-C.Genome biology · 2019Article
- Big data challenges in genome informatics.Biophysical reviews · 2019Article
- Article
- Revealing Gene Function and Transcription Relationship by Reconstructing Gene-Level Chromatin Interaction.Computational and structural biotechnology journal · 2019Article
- Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.Nucleic acids research · 2018Article
- Whole genome sequencing in psychiatric disorders: the WGSPD consortium.Nature neuroscience · 2017Review
- Analysis of the relationship between coexpression domains and chromatin 3D organization.PLoS computational biology · 2017Article
- Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.Genome biology · 2016Article
- QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.PLoS computational biology · 2016Article
- The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer.Frontiers in genetics · 2016Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains challenging. We address this by characterizing the topology of the cortical chromatin interaction network using scale-aware topological measures. We demonstrate that based on these characterizations it is possible to accurately predict spatial co-expression between genes in the mouse cortex. Consistent with previous findings, we find that the chromatin interaction profile of a gene-pair is a good predictor of their spatial co-expression. However, the accuracy of the prediction can be substantially improved when chromatin interactions are described using scale-aware topological measures of the multi-resolution chromatin interaction network. We conclude that, for co-expression prediction, it is necessary to take into account different levels of chromatin interactions ranging from direct interaction between genes (i.e. small-scale) to chromatin compartment interactions (i.e. large-scale).
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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.