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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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GCAS: An Integrated R Package and Shiny App for Comprehensive Cancer Data Analysis.

Jin Wang1, Meidan Wei1, Jiaxin Zhang1

  • 1School of Public Health, Suzhou Medical College of Soochow University, Suzhou 215123, China.

Biomolecules
|June 26, 2026
PubMed
Summary
This summary is machine-generated.

The GEO Cancer Analysis Suite (GCAS) simplifies cancer data analysis, identifying GAPDH as a potential biomarker in lung and breast cancers. It also reveals links between GAPDH, immune cells, and drug sensitivity.

Keywords:
GEO database analysisanticancer drug sensitivitybioinformatics toolcancer biomarker identificationimmune cell infiltration

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Area of Science:

  • Oncology
  • Bioinformatics
  • Genomics

Background:

  • Cancer research faces challenges with complex data and fragmented tools.
  • A unified platform is needed for efficient cancer data analysis and biomarker discovery.
  • Advancing precision medicine requires integrated tools for multi-omics cancer studies.

Purpose of the Study:

  • To develop the GEO Cancer Analysis Suite (GCAS), an R package and Shiny interface.
  • To provide modules for differential gene expression, correlation, pan-cancer, and immune/drug sensitivity analysis.
  • To facilitate biomarker identification, network elucidation, and drug sensitivity prediction in cancer.

Main Methods:

  • Development of GCAS, an R package with a Shiny visualization interface.
  • Implementation of four analysis modules: differential gene expression, correlation, pan-cancer, and immune/drug sensitivity.
  • Application of GCAS to analyze lung and breast cancer datasets, focusing on GAPDH and IGF2BP3.

Main Results:

  • GCAS identified GAPDH upregulation in lung and breast cancers, correlating with IGF2BP3.
  • IGF2BP3 was shown to regulate GAPDH mRNA stability.
  • GAPDH expression negatively correlated with CD4 T cell infiltration and sensitivity to EGFR inhibitors like Erlotinib.

Conclusions:

  • GCAS is a valuable tool for simplifying complex cancer data analysis.
  • The suite enhances the discovery of novel cancer biomarkers, immune profiles, and drug sensitivities.
  • GCAS contributes significantly to advancing cancer research and precision medicine.