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

作者：Zhiting Wei, Duanmiao Si, Bin Duan, Yicheng Gao, Yu Qian, Ling Guo, Qi Liu · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2024 · DOI：10.1101/2024.02.03.578767 · 被引用次数：4 · 研究领域：Single-cell and spatial transcriptomics、Cell Image Analysis Techniques、Gene Regulatory Network Analysis

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, P...