RNAPaceDB: a dedicated database to dissect RNA velocity across diverse cell types.

Area of Science:

• Systems Biology
• Genomics
• Computational Biology

Background:

• RNA velocity offers kinetic insights into gene expression dynamics and cellular state transitions.
• Understanding temporal gene regulation is crucial for identifying biomarkers and therapeutic targets.

Purpose of the Study:

• To introduce RNAPaceDB, a comprehensive database for RNA velocity analysis across diverse cell types.
• To provide a platform for exploring gene expression dynamics and cellular development.

Main Methods:

• Integration of 144 single-cell RNA sequencing datasets (>2.1 million cells, 81 cell types, 41 diseases).
• Generation of 4380 RNA velocity stream plots using six computational models.
• Development of online interfaces for data retrieval and analysis.

Main Results:

• RNAPaceDB enables exploration of RNA velocity profiles for over 18,000 genes.
• The database facilitates analysis of cell development trajectories, differential velocity genes, and functional enrichments.
• It provides insights into cell cluster distribution and regulatory mechanisms.

Conclusions:

• RNAPaceDB is a valuable resource for deciphering the temporal logic of gene expression.
• It supports the discovery of regulatory mechanisms, biomarkers, and therapeutic targets in systems biology and precision medicine.