Identification of key genes related to the prognosis of esophageal squamous cell carcinoma based on chip re-annotation

Meiqi Wang, Dan Liu, Yunchuanxiang Huang, Ziyi Jiang, Feng Wu, Yu Cen, Lan Ma

Research output: Contribution to journalArticlepeer-review

Abstract

Esophageal cancer (EC) is one of the deadliest cancers worldwide. However, reliable biomarkers for early diagnosis, or those for the prognosis of therapy, remain unfulfilled goals for its subtype esophageal squamous cell carcinoma (ESCC). The purpose of this study was to identify reliable biomarkers for the diagnosis and prognosis of ESCC by gene chip re-annotation technique and downstream bioinformatics analysis. In our research, the GSE53624 dataset was downloaded from the GEO database. Then, we reannotated the gene expression probe and obtained the gene expression matrix. Differential expressed genes (DEGs) were found by R packages and they were subjected to Gene Ontology enrichment analysis and protein-protein interaction (PPI) network construction. As a result, a total of 28,885 mRNA probes were reannotated, among which 210 downregulated and 80 up-regulated DEGs were screened out. By combining these genes set in clinical prognosis information and Western blot analysis, we found four genes with diagnostic and prognostic significance, including MMP134SPP1, MMP10, and COL1A1. Furthermore, markers of infiltrating immune cells exhibited different DEG-related immune infiltration patterns.

Original languageEnglish (US)
Article number3229
JournalApplied Sciences (Switzerland)
Volume11
Issue number7
DOIs
StatePublished - Apr 1 2021

Keywords

  • Bioinformatics analyses
  • Chip re-annotation
  • DEGs
  • Esophageal squamous cell carcinoma
  • Prognostic biomarkers

ASJC Scopus subject areas

  • Materials Science(all)
  • Instrumentation
  • Engineering(all)
  • Process Chemistry and Technology
  • Computer Science Applications
  • Fluid Flow and Transfer Processes

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