Identifying Effective Pathways and Genes in Colorectal Cancer according to Stage by Analyzing RNA Sequencing Data

Document Type : Research/Original Article

Authors

1 Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran

2 Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran

3 Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.

10.30476/acrr.2025.107487.1251

Abstract

Introduction: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide.
Numerous studies have demonstrated dysregulated gene expression in CRC. However, comprehensive
investigations are still needed to clarify the underlying biological pathways disrupted by these dysregulated
genes. This study was designed to identify differentially expressed genes (DEGs) common across all CRC
stages compared to normal samples, as well as to identify hub genes and their related pathways.
Methods: RNA sequencing data were downloaded from the TCGA database. Samples were classified into four
stages, and DEGs between each stage and normal samples were identified. Genes present in all four groups
were selected for further analysis. Gene enrichment analyses were performed using the DAVID database to
validate the data. A protein-protein interaction (PPI) network was constructed, and hub genes were identified
using the CytoHubba plugin. The UALCAN database was used to perform in silico validation of the potential
genes of interest.
Results: A total of 2,899 genes were commonly expressed across all four groups. Biological pathway analysis
showed that these genes are enriched in known CRC pathways. PPI network analysis and hub gene identification
using the CytoHubba plugin highlighted key hub genes. Validation through the UALCAN database confirmed
the relevance of these genes, and enrichment analysis demonstrated their association with G protein-coupled
receptor (GPCR) signaling.
Conclusion: The hub genes are functionally associated with the GPCR signaling pathway. Given the welldocumented
involvement of the GPCR pathway in various cancers, especially CRC, further research on these
genes and pathways is essential to enhance our understanding of this disease

Keywords


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