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Related Experiment Video

Updated: Jul 8, 2025

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Identification of Differentially Expressed Genes in Human Colorectal Cancer Using RNASeq Data Validated on the

Aya M A Elsayed1,2,3, Mariam Oweda4, Asmaa M Abushady1,5

  • 1School of Biotechnology, Nile University, Giza, Egypt.

Biochemical Genetics
|December 15, 2023
PubMed
Summary
This summary is machine-generated.

This study identifies novel gene biomarkers for early colorectal cancer (CRC) detection and explores plant-based treatments. The findings highlight potential diagnostic markers and therapeutic avenues for CRC, improving patient outcomes.

Keywords:
Withania somenifraColorectal cancerDEGsDESeq2 packagesGEOGProfilerMMP7RNA-SeqTCF21VEGFD

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Area of Science:

  • Oncology
  • Bioinformatics
  • Molecular Biology

Background:

  • Colorectal cancer (CRC) presents significant global health challenges, with late diagnosis impacting survival rates.
  • Identifying reliable biomarkers is crucial for early detection and improved patient prognosis in CRC.

Purpose of the Study:

  • To develop a bioinformatics pipeline for identifying diagnostic and prognostic biomarkers in colorectal cancer (CRC).
  • To investigate the potential of a plant extract as an alternative or adjunct to chemotherapy for CRC treatment.
  • To validate identified biomarkers and therapeutic targets using molecular and in vitro methods.

Main Methods:

  • Utilized RNA-seq data from cancerous and normal tissues, processed with tools like FastQC, Kallisto, and DESeq2.
  • Employed bioinformatics tools including g:Profiler, GNEMANIA-CytoScape, and CytoHubba for gene enrichment and network analysis.
  • Conducted in vitro experiments with 5-fluorouracil and Withania somnifera extract, alongside molecular docking studies.

Main Results:

  • Identified 1641 differentially expressed genes (DEGs) in CRC, enriched in various signaling pathways.
  • MMP7, TCF21, and VEGFD emerged as promising diagnostic biomarkers for colorectal cancer.
  • Withania somnifera extract showed a positive trend in gene expression and potential therapeutic value, targeting key genes.

Conclusions:

  • The study presents a robust bioinformatics workflow for identifying DEGs as potential CRC biomarkers.
  • MMP7, TCF21, and VEGFD are highlighted as significant diagnostic markers for early CRC detection.
  • Withania somnifera extract demonstrates therapeutic potential in CRC, warranting further investigation for methylation promoter regulation.