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Related Experiment Video

Updated: May 24, 2025

Analyzing Tumor Gene Expression Factors with the CorExplorer Web Portal
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TCGEx: a powerful visual interface for exploring and analyzing cancer gene expression data.

M Emre Kus1, Cagatay Sahin1, Emre Kilic1

  • 1The Department of Molecular Biology and Genetics, Izmir Institute of Technology, 35430, Gulbahce, Izmir, Turkey.

EMBO Reports
|March 3, 2025
PubMed
Summary

The Cancer Genome Explorer (TCGEx) simplifies complex cancer transcriptomics analysis for researchers. This web tool identifies microRNAs and cytokine genes predicting immune checkpoint inhibitor response, aiding cancer research and treatment strategies.

Keywords:
Functional GenomicsGene ExpressionInteractive AnalysisMachine LearningTCGA

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Area of Science:

  • Bioinformatics
  • Cancer Genomics
  • Computational Biology

Background:

  • Analyzing large-scale cancer gene expression data, such as from The Cancer Genome Atlas (TCGA), often requires advanced programming expertise, limiting accessibility for many researchers.
  • Existing tools may lack the integrated functionality for diverse analyses like survival modeling, gene set enrichment, and machine learning on transcriptomic data.

Purpose of the Study:

  • To develop and introduce The Cancer Genome Explorer (TCGEx), a user-friendly, web-based platform designed to democratize sophisticated analyses of cancer transcriptomics data.
  • To enable researchers to explore molecular subtypes of human melanoma, identify immune-related biomarkers, and predict responses to immune checkpoint inhibitors.

Main Methods:

  • Development of TCGEx using the R/Shiny framework, providing access to preprocessed TCGA and immune checkpoint inhibition data.
  • Integration of user-uploaded datasets and implementation of advanced analytical modules including survival modeling, gene set enrichment analysis, unsupervised clustering, and machine learning.
  • Validation of findings using independent clinical trial data for melanoma and other cancers.

Main Results:

  • TCGEx facilitates the exploration of molecular subsets within human melanoma, identifying microRNAs linked to intratumoral immunity.
  • The platform successfully identified cytokine genes capable of predicting patient responses to immune checkpoint inhibitors prior to treatment.
  • Analyses performed using TCGEx were validated against independent clinical trial data, confirming the reliability of identified biomarkers.

Conclusions:

  • TCGEx provides an accessible and powerful tool for researchers to extract meaningful insights from cancer transcriptomics data without extensive coding knowledge.
  • The platform supports the discovery of novel biomarkers, such as microRNAs and cytokines, that can inform personalized treatment strategies for cancer patients undergoing immunotherapy.
  • TCGEx enhances the utility of public cancer genomics datasets, fostering further research into cancer biology and therapeutic development.