Ruan Zhihan, Lin Fan, Zhang Zhenjie, Cao Jiayue, Xiang Wenting, Wei Xiaoyi, Liu Jian
Centre for Bioinformatics and Intelligent Medicine, College of Computer Science, Nankai University, No.38 Tongyan Road, 300350 Tianjin, China.
Fifth Affiliated Hospital of Sun Yat-sen University, No.52 East Meihua Road, 519000 Zhuhai, China.
Nucleic Acids Res. 2025 Jan 6;53(D1):D1087-D1098. doi: 10.1093/nar/gkae986.
Paired single-cell and spatially resolved transcriptomics (SRT) data supplement each other, providing in-depth insights into biological processes and disease mechanisms. Previous SRT databases have limitations in curating sufficient single-cell and SRT pairs (SC-SP pairs) and providing real-time heuristic analysis, which hinder the effort to uncover potential biological insights. Here, we developed Pairpot (http://pairpot.bioxai.cn), a database tailored for paired single-cell and SRT data with real-time heuristic analysis. Pairpot curates 99 high-quality pairs including 1,425,656 spots from 299 datasets, and creates the association networks. It constructs the curated pairs by integrating multiple slices and establishing potential associations between single-cell and SRT data. On this basis, Pairpot adopts semi-supervised learning that enables real-time heuristic analysis for SC-SP pairs where Lasso-View refines the user-selected SRT domains within milliseconds, Pair-View infers cell proportions of spots based on user-selected cell types in real-time and Layer-View displays SRT slices using a 3D hierarchical layout. Experiments demonstrated Pairpot's efficiency in identifying heterogeneous domains and cell proportions.
配对的单细胞和空间分辨转录组学（SRT）数据相互补充，为深入了解生物过程和疾病机制提供了依据。先前的SRT数据库在整理足够的单细胞和SRT对（SC-SP对）以及提供实时启发式分析方面存在局限性，这阻碍了挖掘潜在生物学见解的努力。在此，我们开发了Pairpot（http://pairpot.bioxai.cn），这是一个专为配对单细胞和SRT数据量身定制的数据库，并具有实时启发式分析功能。Pairpot整理了99个高质量对，包括来自299个数据集的1,425,656个斑点，并创建了关联网络。它通过整合多个切片并在单细胞和SRT数据之间建立潜在关联来构建整理后的对。在此基础上，Pairpot采用半监督学习，能够对SC-SP对进行实时启发式分析，其中Lasso-View可在毫秒内优化用户选择的SRT域，Pair-View可根据用户选择的细胞类型实时推断斑点的细胞比例，而Layer-View则使用三维分层布局显示SRT切片。实验证明了Pairpot在识别异质域和细胞比例方面的效率。
