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Cistrome Data Browser: integrated search, analysis and visualization of chromatin data
Len Taing1, Ariaki Dandawate2, Sehi L'Yi3
1Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA.
Nucleic Acids Research
|November 16, 2023
Summary
The Cistrome Data Browser (Cistrome DB) v3.0 offers extensive human and mouse epigenomic data, including ChIP-seq and ATAC-seq. This updated resource enhances genome-wide regulatory element analysis with improved visualization and search capabilities.
Area of Science:
- Genomics
- Epigenetics
- Bioinformatics
Background:
- The Cistrome Data Browser is a curated resource for epigenomic data.
- It previously provided access to ChIP-seq, ATAC-seq, and DNase-seq data for humans and mice.
- The previous version facilitated the study of genome-wide regulatory element locations.
Purpose of the Study:
- To release Cistrome DB version 3.0, an updated and expanded resource for epigenomic data analysis.
- To improve the user interface and search functionalities for more effective data retrieval and visualization.
- To provide enhanced tools for predicting gene regulators and understanding cis-regulatory element function.
Main Methods:
- Compilation and integration of approximately 32,000 new human and mouse epigenomic datasets.
- Development of a single-page application user interface with unified search functions.
- Implementation of an embedded genome browser for data visualization.
- Expansion of quality control statistics, sequence logo incorporation, and metadata enrichment.
Main Results:
- Cistrome DB v3.0 contains approximately 45,000 human and 44,000 mouse samples.
- The new version offers improved data search, including keyword, menu, and data-driven options.
- Enhanced visualization tools allow prediction of gene regulators and cis-regulatory element functionality.
- Expanded quality control, sequence logos, and sample metadata are now available.
Conclusions:
- Cistrome DB v3.0 represents a significant expansion and improvement of the Cistrome Data Browser resource.
- The updated platform facilitates more effective analysis and interpretation of genome-wide epigenomic data.
- This resource will aid researchers in understanding gene regulation and chromatin accessibility in humans and mice.
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