# GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data

## TL;DR

GeneSurfer is a tool that helps researchers explore gene co-expression patterns in 3D spatial transcriptomics data, offering insights into biological functions and supporting hypothesis generation.

## Contribution

GeneSurfer introduces an interactive interface for localized transcriptome-wide gene co-expression analysis in 3D spatial transcriptomics data.

## Key findings

- GeneSurfer identifies and annotates localized co-expression patterns in spatial transcriptomics data.
- The tool supports multi-slice 3D rendering and on-the-fly Gene Ontology term annotation of gene clusters.
- It is demonstrated to be effective using data from the Allen Brain Cell Atlas.

## Abstract

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.

•An interactive visualization tool to explore transcriptome-wide gene co-expression•On-the-fly gene filtering and clustering within transcriptomically similar cells•On-the-fly GO annotation links gene clusters to biological functions•Compatible with large-scale spatial transcriptomics datasets in 2D and 3D

An interactive visualization tool to explore transcriptome-wide gene co-expression

On-the-fly gene filtering and clustering within transcriptomically similar cells

On-the-fly GO annotation links gene clusters to biological functions

Compatible with large-scale spatial transcriptomics datasets in 2D and 3D

Bioinformatics; Complex system biology; Transcriptomics