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

Abstract

Single-cell perturbation sequencing techniques (scPerturbation), represented by single cell genetic perturbation sequencing (e.g., Perturb-seq) and single cell chemical perturbation sequencing (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 functions and mechanisms in complex biological systems at an unprecedented resolution. Despite these advancements, a notable gap exists in the availability of a dedicated database for exploring and querying scPerturbation data. To address this gap and facilitate seamless data sharing for researchers, we present PerturBase--the first and most comprehensive database designed for the analysis and visualization of scPerturbation data (http://www.perturbase.cn/). PerturBase consolidates 122 datasets from 46 publicly accessible research studies, covering 115 single-modal and 7 multi-modal datasets that include 24254 genetic and 230 chemical perturbations from about 6 million cells. The database provides insights through various software-analyzed results, encompassing quality control, denoising, differential expression gene analysis, perturbation function analysis, and correlation characterization between perturbations. All datasets and in-depth analyses are presented in user-friendly, easy-to-browse pages and can be visualized through intuitive tables and various image formats. In summary, PerturBase stands as a pioneering high-content database, intended for searching, visualizing, and analyzing scPerturbation datasets, contributing to an enhanced understanding of perturbation functions and mechanisms. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/578767v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@15bdfcborg.highwire.dtl.DTLVardef@c1be77org.highwire.dtl.DTLVardef@1bf7e32org.highwire.dtl.DTLVardef@f62e8b_HPS_FORMAT_FIGEXP M_FIG C_FIG