Li Chang, Thijssen Julian, Kroes Thomas, van der Burg Ximaine, van der Weerd Louise, Höllt Thomas, Lelieveldt Boudewijn
Department of Radiology, Leiden University Medical Center, ZA Leiden 2333, the Netherlands.
Department of Human Genetics, Leiden University Medical Center, ZA Leiden 2333, the Netherlands.
iScience. 2025 Jun 6;28(7):112713. doi: 10.1016/j.isci.2025.112713. eCollection 2025 Jul 18.
Gene co-expression provides crucial insights into biological functions, however, there is a lack of exploratory analysis tools for localized gene co-expression in large-scale datasets. We present GeneSurfer, an interactive interface designed to explore localized transcriptome-wide gene co-expression patterns in the 3D spatial domain. Key features of GeneSurfer include transcriptome-wide gene filtering and gene clustering based on spatial local co-expression within transcriptomically similar cells, multi-slice 3D rendering of average expression of gene clusters, and on-the-fly Gene Ontology term annotation of co-expressed gene sets. Additionally, GeneSurfer offers multiple linked views for investigating individual genes or gene co-expression in the spatial domain at each exploration stage. Demonstrating its utility with both spatially resolved transcriptomics and single-cell RNA sequencing data from the Allen Brain Cell Atlas, GeneSurfer effectively identifies and annotates localized transcriptome-wide co-expression, providing biological insights and facilitating hypothesis generation and validation.
基因共表达为生物学功能提供了至关重要的见解，然而，在大规模数据集中缺乏用于局部基因共表达的探索性分析工具。我们展示了GeneSurfer，这是一个交互式界面，旨在探索三维空间域中全转录组范围的局部基因共表达模式。GeneSurfer的关键特性包括全转录组范围的基因筛选以及基于转录组相似细胞内空间局部共表达的基因聚类、基因簇平均表达的多层三维渲染，以及对共表达基因集的即时基因本体术语注释。此外，GeneSurfer在每个探索阶段都提供多个关联视图，用于在空间域中研究单个基因或基因共表达。通过来自艾伦脑图谱的空间分辨转录组学和单细胞RNA测序数据展示了其效用，GeneSurfer有效地识别并注释了全转录组范围的局部共表达，提供了生物学见解并促进了假设的产生和验证。
