iGPSC-DB: a comprehensive database for an inferred single-cell genetic perturbation atlas
Peng Wang, Zhe Chen, Yifang Zhang, Anhui Kang, Jiangtao Xing, Xinyi Wang, Longqi Xu, Siyao Lu, Xinyu Song, Qiuyan Guo, Yanjun Xu, Feng LiAbstract
Genetic perturbation-induced transcriptional reprogramming drastically remodels tumor cellular phenotypes and tumor microenvironment crosstalk. Unraveling the heterogeneous cellular responses to genetic perturbations is essential for the mechanistic dissection of tumors and the discovery of therapeutic targets. Here, we present iGPSC-DB (https://bio-bigdata.hrbmu.edu.cn/iGPSC-DB), a database designed to infer connections between tumor microenvironmental cells and diverse genetic perturbation events and to dissect the heterogeneous cellular responses to these perturbations. iGPSC-DB curates associations linking 178 114 perturbation events that target 7407 genes to 9 249 080 single cells from 1580 samples across 88 cancer types. iGPSC-DB also provides seven user-friendly tools for retrieving and analyzing: (i) inferred associations between genetic perturbation events and cells/cell types; (ii) the inferred perturbation–associated effects of perturbations on cellular functions, developmental trajectories, and cell–cell communication within the tissue microenvironment; (iii) the combined effects of different perturbations on cells, facilitating the design of combination therapeutic regimens; (iv) the impact of different perturbations on the differentiation trajectories and functional states of malignant cells; and (v) the association between perturbed target genes and clinical survival outcomes. iGPSC-DB will serve as a valuable resource to advance single-cell-resolution research on gene functions, regulatory mechanisms, and the discovery of tumor therapeutic targets.