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

Abstract

RNA velocity, which reflects the balance between nascent RNA synthesis and mature RNA degradation, provides a kinetic perspective to explore gene expression dynamics and cellular state transitions, offering profound insights into diverse biological processes and disease mechanisms. Deciphering RNA velocity patterns across cell types and contexts will deepen our understanding of the temporal logic of gene regulation and facilitating the discovery of novel biomarkers and therapeutic targets. Here, we present RNAPaceDB (http://biocclab.cn/RNAPaceDB/), a dedicated database to dissect RNA velocity across diverse cell types. RNAPaceDB integrates single-cell RNA sequencing profiles from 144 datasets, encompassing over 2.1 million cells across 81 cell types and 41 diseases, and offers 4380 velocity stream plots derived from six computational models. Using RNAPaceDB, users can explore RNA velocity profiles of >18 000 genes across cell development processes. Additionally, RNAPaceDB provides integrated online interfaces to retrieve and analyze cell cluster distribution, cell development trajectories, cell type-specific differential velocity genes, and functional enrichments under varying conditions. Collectively, RNAPaceDB serves as a valuable resource for deciphering the temporal logic of gene expression dynamics, facilitating discoveries of regulatory mechanisms, biomarkers, and therapeutic targets in precision medicine and systems biology.