Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools

Area of Science:

• Bioinformatics
• Comparative Genomics
• Developmental Biology

Background:

• Bgee is a database for comparative gene expression patterns across animal species.
• Consistent data annotation and processing enable cross-species comparisons.
• Previous versions lacked comprehensive single-cell RNA sequencing data integration.

Purpose of the Study:

• To integrate single-cell RNA sequencing data into Bgee for cell-resolution gene expression analysis.
• To enhance cross-species gene expression data comparability.
• To improve data accessibility and query capabilities for researchers.

Main Methods:

• Curated integration of public single-cell RNA sequencing datasets.
• Development of a new web interface with advanced querying features.
• Expansion of species coverage and update of programmatic access tools.

Main Results:

• Bgee now provides definitive, cell-resolution gene expression patterns comparable across species.
• A new user-friendly interface allows detailed data retrieval by organ, cell type, and developmental stage.
• Species count increased from 29 to 52, including fish, livestock, and nonhuman primates.

Conclusions:

• Bgee offers a powerful, unified resource for comparative gene expression studies at single-cell resolution.
• The updated platform enhances biological research by providing accessible and detailed cross-species data.
• Expanded species coverage supports diverse research areas, from vertebrate genomics to agricultural science.