EXPRESSO: a multi-omics database to explore multi-layered 3D genomic organization.

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• The three-dimensional (3D) genome organization is critical for gene regulation.
• Understanding the interplay between 3D genome structure and gene expression requires integrated multi-omics data.

Purpose of the Study:

• To introduce EXPRESSO, a novel multi-omics database for exploring and visualizing 3D genomic features across 46 human tissues.
• To provide a comprehensive resource for studying the relationship between 3D genome architecture and transcriptional regulation.

Main Methods:

• Integration of 1360 3D genomic datasets (Hi-C, HiChIP, ChIA-PET) and 842 1D genomic/transcriptomic datasets (ChIP-seq, ATAC-seq, RNA-seq) from matched biosamples.
• Development of a user-friendly interface for data exploration, visualization, and download.
• Implementation of RESTful APIs for programmatic access and web-based applications for correlating genomic features with gene expression.

Main Results:

• EXPRESSO offers diverse 3D genomic feature types, including compartments, contact matrices, domains, stripes, and chromatin loops.
• The database provides advanced visualization tools and web applications to explore multi-layered 3D genomic data.
• Programmatic access via RESTful APIs allows for advanced data retrieval and analysis.

Conclusions:

• EXPRESSO serves as a vital, freely available resource for the research community to deepen understanding of 3D genome architecture.
• The database facilitates research into the implications of 3D genome organization for human health and disease.
• EXPRESSO enables comprehensive exploration of the relationship between spatial genome organization and gene regulation.