iGPSC-DB: a comprehensive database for an inferred single-cell genetic perturbation atlas
- 1College of Bioinformatics Science and Technology, Harbin Medical University , 157 Baojian Road, Harbin 150081 ,
- 2Department of Gynecology, The First Affiliated Hospital of Harbin Medical University , Harbin 150081 ,
Abstract
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.
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BibTeX
@article{wang2026igpscdb,
title = {{iGPSC-DB: a comprehensive database for an inferred single-cell genetic perturbation atlas}},
author = {Peng Wang and Zhe Chen and Yifang Zhang and Anhui Kang and Jiangtao Xing and Xinyi Wang and Longqi Xu and Siyao Lu and Xinyu Song and Qiuyan Guo and Yanjun Xu and Feng Li},
journal = {Nucleic Acids Research},
year = {2026},
month = nov,
doi = {10.1093/nar/gkag1079},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1079/9012874},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - iGPSC-DB: a comprehensive database for an inferred single-cell genetic perturbation atlas
AU - Peng Wang
AU - Zhe Chen
AU - Yifang Zhang
AU - Anhui Kang
AU - Jiangtao Xing
AU - Xinyi Wang
AU - Longqi Xu
AU - Siyao Lu
AU - Xinyu Song
AU - Qiuyan Guo
AU - Yanjun Xu
AU - Feng Li
PY - 2026
DA - 2026/11/05
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1079
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1079/9012874
AB - 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.
SN - 0305-1048
SN - 1362-4962
ER -