HiCHub: A Network-Based Approach to Identify Domains of Differential Interactions from 3D Genome Data
Peng, W.; Yuan, S.; Li, X.; Zhu, S.; Xue, H.
Show abstract
Chromatin architecture is important for gene regulation. Existing algorithms for the identification of interactions changes focus on loops between focal loci. Here we develop a network-based algorithm HiCHub to detect chromatin interaction changes at larger scales. It identifies clusters of genomic elements in physical proximity in one state that exhibit concurrent decreases in interaction among them in the opposite state. The hubs exhibit concordant changes in chromatin state and expression changes, supporting their biological significance. HiCHub works well with data of limited sequencing coverage and facilitates the integration of the one-dimensional epigenetic landscape onto the chromatin architecture. HiCHub provides an approach for finding extended architectural changes and contributes to the connection with transcriptional output. HiCHub is freely available at https://github.com/WeiqunPengLab/HiCHub.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions 96%
- Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation 95%
- Stripenn detects architectural stripes from chromatin conformation data using computer vision 95%
Similar papers in this journal
Similar papers in this journal
- Neuron types in the developing mouse CNS can be divided into several epigenomic and transcriptomic classes 94%
- Epigenetic control of metabolic identity across cell types 92%
- A Machine Learning One-Class Logistic Regression Model to Predict Stemness in Single Cell Transcriptomics and Spatial Omics Datasets 92%
Similar papers in this journal
- Z-Flipons conserved between human and mouse are associated with increased transcription initiation rates 95%
- Functional buffering via cell-specific gene expression promotes tissue homeostasis and cancer robustness 94%
- Active regulatory elements recruit cohesin to establish cell-specific chromatin domains. 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.