SDMap: a comprehensive database of spatial drug perturbation maps.

IF 13.1 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2025-10-22 DOI:10.1093/nar/gkaf1046

Feng Li,Zhe Chen,Yifang Zhang,Xinguo Ye,Wenli Fan,Anhui Kang,Xinyu Song,Liying Pei,Quan Qi,Wensong Liu,Zhengliang Zha,Yunpeng Zhang,Chunlong Zhang,Yanjun Xu

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引用次数: 0

Abstract

The arrangement patterns and spatial distribution features of cells within tissues are key regulators of drug actions and cellular responses; however, the specific spatial microenvironment that mediates drug actions and efficacy remains to be elucidated. Here, we introduce SDMap (http://bio-bigdata.hrbmu.edu.cn/SDMap/), a database to dissect the spatial distributions of drug-associated cells and spatial contexts that contribute to drug actions. SDMap establishes connections between 5 490 079 spatial locations (spots/cells) derived from 989 slices of 35 human tissues (including disease-state slices) and 538 419 instances across 33 149 drugs. It also offers 10 user-friendly tools for retrieving and analyzing: (i) associations between drug-associated instances and spatial spots/cells, niches, or cell types; (ii) the influence of spatial drug target activity on drug actions; (iii) drug-associated instances exhibiting highly variable spatial perturbation effects; (iv) the perturbation effects of drug dosage and duration on the spatial microenvironment; (v) spatial differentiation trajectories of drug-perturbed cells; (vi) the impact of spatial cellular functional activity on drug perturbation; (vii) spatial perturbation effect maps of drug combinations; and (viii) 3D maps of drug perturbation effects within spatial tissue contexts. SDMap is anticipated to yield critical insights into how spatial heterogeneity influences drug actions, and serve as a comprehensive database for identifying spatially resolved precision therapy targets and elucidating drug-associated mechanisms.

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SDMap：空间药物摄动图的综合数据库。

组织内细胞的排列模式和空间分布特征是药物作用和细胞反应的关键调节因子；然而，介导药物作用和疗效的具体空间微环境仍有待阐明。在这里，我们介绍SDMap (http://bio-bigdata.hrbmu.edu.cn/SDMap/)，这是一个数据库，用于剖析药物相关细胞的空间分布和有助于药物作用的空间背景。SDMap建立了来自35个人体组织（包括疾病状态切片）的989个切片的549079个空间位置（点/细胞）与33 149种药物的538419个实例之间的联系。它还提供了10种用户友好的工具，用于检索和分析：(i)药物相关实例与空间点/细胞、壁龛或细胞类型之间的关联；（二）空间药物靶点活性对药物作用的影响；（三）与药物有关的实例表现出高度可变的空间扰动效应；(4)药物剂量和持续时间对空间微环境的扰动效应；(v)药物干扰细胞的空间分化轨迹；（vi）空间细胞功能活动对药物扰动的影响；（vii）药物组合的空间摄动效果图；（viii）空间组织环境中药物扰动效应的3D图。SDMap有望对空间异质性如何影响药物作用产生重要见解，并作为识别空间分辨精确治疗靶点和阐明药物相关机制的综合数据库。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.