PerturBase: a comprehensive database for single-cell perturbation data analysis and visualization

Nucleic Acids Res. 2024 Oct 8:gkae858. doi: 10.1093/nar/gkae858. Online ahead of print.

ABSTRACT

Single-cell perturbation (scPerturbation) sequencing techniques, represented by single-cell genetic perturbation (e.g. Perturb-seq) and single-cell chemical perturbation (e.g. sci-Plex), result from the integration of single-cell toolkits with conventional bulk screening methods. These innovative sequencing techniques empower researchers to dissect perturbation effects in biological systems at an unprecedented resolution. Despite these advancements, a notable gap exists in the availability of a dedicated database for exploring scPerturbation data. To address this gap, we present PerturBase, the most comprehensive database designed for the analysis and visualization of scPerturbation data (http://www.perturbase.cn/). PerturBase curates 122 datasets from 46 publicly available studies, covering 115 single-modal and 7 multi-modal datasets that include 24 254 genetic and 230 chemical perturbations from approximately 5 million cells. The database, comprising the 'Dataset' and 'Perturbation' modules, provides insights into various results, encompassing quality control, denoising, differential gene expression analysis, functional analysis of perturbation effects and characterization of relationships between perturbations. All the datasets and results are presented on user-friendly, easy-to-browse web pages and can be visualized through intuitive and interactive plot and table formats. In summary, PerturBase stands as a pioneering, high-content database intended for searching, visualizing and analyzing scPerturbation datasets, contributing to a deeper understanding of perturbation effects.

PMID:39377396 | DOI:10.1093/nar/gkae858