iScience
GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data
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.
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@article{bib:li:2025,
author = { Li, Chang and Thijssen, Julian and Kroes, Thomas and van der Burg, Ximaine and van der Weerd, Louise and Höllt, Thomas and Lelieveldt, Boudewijn P. F. },
title = { GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data },
journal = { iScience },
year = { 2025 },
pages = { 112713 },
publisher = { Cell Press },
doi = { 10.1101/2024.07.05.602230 },
pubmedid = { 39005368 },
url = { https://publications.graphics.tudelft.nl/papers/818 },
}