spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis.
Document Type
Article
Publication Date
3-3-2025
Identifier
DOI: 10.1158/0008-5472.CAN-24-2346; PMCID: PMC11873723
Abstract
Spatial transcriptomics (ST) is a powerful tool for understanding tissue biology and disease mechanisms. However, the advanced data analysis and programming skills required can hinder researchers from realizing the full potential of ST. To address this, we developed spatialGE, a web application that simplifies the analysis of ST data. The application spatialGE provided a user-friendly interface that guides users without programming expertise through various analysis pipelines, including quality control, normalization, domain detection, phenotyping, and multiple spatial analyses. It also enabled comparative analysis among samples and supported various ST technologies. The utility of spatialGE was demonstrated through its application in studying the tumor microenvironment of two data sets: 10× Visium samples from a cohort of melanoma metastasis and NanoString CosMx fields of vision from a cohort of Merkel cell carcinoma samples. These results support the ability of spatialGE to identify spatial gene expression patterns that provide valuable insights into the tumor microenvironment and highlight its utility in democratizing ST data analysis for the wider scientific community. Significance: The spatialGE web application enables user-friendly exploratory analysis of spatial transcriptomics data by using a point-and-click interface to guide users from data input to discovery of spatial patterns, facilitating hypothesis generation.
Journal Title
Cancer research
Volume
85
Issue
5
First Page
848
Last Page
858
MeSH Keywords
Humans; Tumor Microenvironment; Melanoma; Gene Expression Profiling; Transcriptome; Software; Internet; Carcinoma, Merkel Cell; Skin Neoplasms; User-Computer Interface; Data Analysis
PubMed ID
39636739
Keywords
Tumor Microenvironment; Melanoma; Gene Expression Profiling; Transcriptome; Software; Internet; Merkel Cell Carcinoma; Skin Neoplasms; User-Computer Interface; Data Analysis
Recommended Citation
Ospina OE, Manjarres-Betancur R, Gonzalez-Calderon G, et al. spatialGE Is a User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis. Cancer Res. 2025;85(5):848-858. doi:10.1158/0008-5472.CAN-24-2346
Comments
Grants and funding
This open access article is distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license.
Publisher's Link: https://aacrjournals.org/cancerres/article/85/5/848/751992/spatialGE-Is-a-User-Friendly-Web-Application-That