Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• The Cistrome Data Browser (DB) is a key resource for cis-regulatory information.
• It integrates data from ChIP-seq, DNase-seq, and ATAC-seq assays.
• These assays map genome-wide locations of regulatory elements.

Purpose of the Study:

• To update and expand the Cistrome DB with new datasets.
• To introduce a new Toolkit module for enhanced data analysis.
• To provide researchers with improved tools for exploring cis-regulatory data.

Main Methods:

• The Cistrome DB aggregates approximately 47,000 human and mouse samples.
• A new Toolkit module offers features for querying regulatory factors, genomic intervals, and sample similarity.
• Data is derived from ChIP-seq, DNase-seq, and ATAC-seq chromatin profiling.

Main Results:

• The Cistrome DB now contains ~47,000 human and mouse samples, with 24,000 new datasets.
• The Toolkit enables users to identify regulatory factors for specific genes.
• The Toolkit facilitates searches for factor binding, histone modifications, and chromatin accessibility within genomic intervals.
• It also allows for comparison of user-provided genomic intervals with existing datasets.

Conclusions:

• The updated Cistrome DB and its new Toolkit provide a valuable, user-friendly resource.
• These tools will significantly aid the biomedical research community in analyzing cis-regulatory information.
• The database and Toolkit are freely accessible online.