Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation.
BMC Bioinformatics
; 24(1): 102, 2023 Mar 20.
Article
in En
| MEDLINE
| ID: mdl-36941541
ABSTRACT
BACKGROUND:
Epigenetic modification of chromatin plays a pivotal role in regulating gene expression during cell differentiation. The scale and complexity of epigenetic data pose significant challenges for biologists to identify the regulatory events controlling cell differentiation.RESULTS:
To reduce the complexity, we developed a package, called Snapshot, for clustering and visualizing candidate cis-regulatory elements (cCREs) based on their epigenetic signals during cell differentiation. This package first introduces a binarized indexing strategy for clustering the cCREs. It then provides a series of easily interpretable figures for visualizing the signal and epigenetic state patterns of the cCREs clusters during the cell differentiation. It can also use different hierarchies of cell types to highlight the epigenetic history specific to any particular cell lineage. We demonstrate the utility of Snapshot using data from a consortium project for ValIdated Systematic IntegratiON (VISION) of epigenomic data in hematopoiesis.CONCLUSION:
The package Snapshot can identify all distinct clusters of genomic locations with unique epigenetic signal patterns during cell differentiation. It outperforms other methods in terms of interpreting and reproducing the identified cCREs clusters. The package of Snapshot is available at GitHub https//github.com/guanjue/Snapshot .Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Chromatin
/
Epigenomics
Type of study:
Prognostic_studies
Language:
En
Journal:
BMC Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2023
Document type:
Article
Affiliation country:
Estados Unidos