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Updated: Feb 10, 2026

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

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Gene expression profiles and pathway enrichment analysis of human osteosarcoma cells exposed to sorafenib

Zhehao Dai1, Haoyu Tang2, Yue Pan1

  • 1Department of Spine Surgery The Second Xiangya Hospital Central South University Changsha China.

FEBS Open Bio
|May 11, 2018
PubMed

Insights

Sorafenib, a tyrosine kinase inhibitor, impacts osteosarcoma by altering inflammatory and angiogenesis pathways. Key genes like PGF were identified, offering new therapeutic targets for this cancer.

Area of Science:

  • Oncology
  • Molecular Biology
  • Bioinformatics

Background:

  • Sorafenib is a multi-kinase inhibitor used in treating various cancers.
  • Its precise mechanism in osteosarcoma remains incompletely understood.
  • Identifying key molecular targets is crucial for optimizing osteosarcoma treatment.

Purpose of the Study:

  • To identify key genes, enriched pathways, and critical modules in human osteosarcoma cells treated with sorafenib.
  • To elucidate the molecular mechanisms underlying sorafenib's effects on osteosarcoma.
  • To uncover potential novel therapeutic targets for osteosarcoma.

Main Methods:

  • Gene expression profiles of osteosarcoma cells exposed to sorafenib were analyzed using data from the GEO database (GSE53155).
  • Differentially expressed genes (DEGs) were identified using R bioconductor packages.
  • Functional enrichment analyses (DAVID database) and protein-protein interaction network construction (STRING, Cytoscape) were performed.

Main Results:

  • Sixty-one differentially expressed genes (DEGs) were identified.
  • Enrichment analysis revealed significant involvement of inflammatory immune response and angiogenesis pathways.
  • Eight hub genes were identified, including IL8, CXCL2, PTGS2, FOS, CXCL1, C3, EHMT2, and PGF. A key module highlighted PGF as the seed gene.

Conclusions:

  • This study reveals that sorafenib influences osteosarcoma through modulation of inflammatory and angiogenesis pathways.
  • Key genes such as PGF, CXCL1, and CXCL2 are central to sorafenib's mechanism in osteosarcoma.
  • The findings provide a foundation for understanding novel therapeutic strategies and targets for osteosarcoma treatment.
Keywords:
bioinformaticsfunctional enrichment analysisosteosarcomasorafenib

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