Open Access

Identification of crucial genes associated with esophageal squamous cell carcinoma by gene expression profile analysis

  • Authors:
    • Xuehai Wang
    • Gang Li
    • Qingsong Luo
    • Chongzhi Gan
  • View Affiliations

  • Published online on: April 11, 2018     https://doi.org/10.3892/ol.2018.8464
  • Pages: 8983-8990
  • Copyright: © Wang et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

To uncover the genes associated with the development of esophageal squamous cell carcinoma (ESCC), an ESCC microarray dataset was used to identify genes differentially expressed between ESCC and normal control tissues. The dataset GSE17351 was downloaded from the Gene Expression Omnibus, containing 5 tumor esophageal mucosa samples and 5 adjacent normal esophageal mucosa samples from 5 male patients with ESCC. The differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Data R package. Then, a co‑expression network was constructed using the Weighted Correlation Network Analysis (WGCNA) package, and co‑expression network modules were obtained with a hierarchical clustering algorithm. Additionally, functional enrichment analyses for DEGs in the top 2 modules with the highest significance were respectively conducted using the WGCNA package and the cluster Profiler package. In total, 487 upregulated and 468 downregulated DEGs were identified. A total of 24 modules were obtained from the co‑expression network, and the top 2 modules with the highest significance, designated as ‘blue4’ and ‘magenta’, were further analyzed. In the module blue4, DEGs were significantly enriched in a number of Gene Ontology terms, including ‘spindle organization’ [e.g., ubiquitin conjugating enzyme E2 C (UBE2C) and SAC3 domain containing 1] and ‘cell cycle process’ [e.g., UBE2C, minichromosome maintenance complex component 6 (MCM6) and cell division cycle 20 (CDC20)]. Furthermore, a number of DEGs (e.g., UBE2C, CDC20 and MCM6) were enriched in the ‘cell cycle’ and ‘ubiquitin mediated proteolysis’ pathways. In the module ‘magenta’, a number of DEGs [e.g., transferrin receptor (TFRC) and TEA domain transcription factor 4 (TEAD4)] were enriched in the primary metabolic process and intracellular membrane‑bounded organelle. Additionally, 308 upregulated genes and 215 downregulated genes were differentially expressed in the same pattern in another dataset, GSE20347, including UBE2C, CDC20, MCM6, TFRC, TEAD4, protein phosphatase 1 regulatory subunit 3C and MAL, T‑cell differentiation protein. These DEGs may function in the development of ESCC.
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June-2018
Volume 15 Issue 6

Print ISSN: 1792-1074
Online ISSN:1792-1082

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Spandidos Publications style
Wang X, Li G, Luo Q and Gan C: Identification of crucial genes associated with esophageal squamous cell carcinoma by gene expression profile analysis. Oncol Lett 15: 8983-8990, 2018
APA
Wang, X., Li, G., Luo, Q., & Gan, C. (2018). Identification of crucial genes associated with esophageal squamous cell carcinoma by gene expression profile analysis. Oncology Letters, 15, 8983-8990. https://doi.org/10.3892/ol.2018.8464
MLA
Wang, X., Li, G., Luo, Q., Gan, C."Identification of crucial genes associated with esophageal squamous cell carcinoma by gene expression profile analysis". Oncology Letters 15.6 (2018): 8983-8990.
Chicago
Wang, X., Li, G., Luo, Q., Gan, C."Identification of crucial genes associated with esophageal squamous cell carcinoma by gene expression profile analysis". Oncology Letters 15, no. 6 (2018): 8983-8990. https://doi.org/10.3892/ol.2018.8464