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Integrated bioinformatic analysis unveils significant genes and pathways in the pathogenesis of supratentorial primitive neuroectodermal tumor

Authors Wang G, Li L, Liu B, Han X, Wang CH, Wang JW

Received 10 August 2017

Accepted for publication 25 October 2017

Published 4 April 2018 Volume 2018:11 Pages 1849—1859


Checked for plagiarism Yes

Review by Single anonymous peer review

Peer reviewer comments 2

Editor who approved publication: Dr Carlos E Vigil

Guang-Yu Wang,1,* Ling Li,2,* Bo Liu,1 Xiao Han,1 Chun-Hua Wang,1 Ji-Wen Wang3

1Department of Neurosurgery, 2Department of Pediatrics, Qilu Children’s Hospital of Shandong University, Jinan, Shandong, 3Department of Neurology, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Pudong New District, Shanghai, People’s Republic of China

*These authors contributed equally to this work

Purpose: This study aimed to explore significant genes and pathways involved in the pathogenesis of supratentorial primitive neuroectodermal tumor (sPNET).
Materials and methods: Gene expression profile of GSE14295 was downloaded from publicly available Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened out in primary sPNET samples compared with normal fetal and adult brain reference samples (sPNET vs fetal brain and sPNET vs adult brain). Pathway enrichment analysis of these DEGs was conducted, followed by protein–protein interaction (PPI) network construction and significant module selection. Additionally, transcription factors (TFs) regulating the common DEGs in the two comparison groups were identified, and the regulatory network was constructed.
Results: In total, 526 DEGs (99 up- and 427 downregulated) in sPNET vs fetal brain and 815 DEGs (200 up- and 615 downregulated) in sPNET vs adult brain were identified. DEGs in sPNET vs fetal brain and sPNET vs adult brain were associated with calcium signaling pathway, cell cycle, and p53 signaling pathway. CDK1, CDC20, BUB1B, and BUB1 were hub nodes in the PPI networks of DEGs in sPNET vs fetal brain and sPNET vs adult brain. Significant modules were extracted from the PPI networks. In addition, 64 upregulated and 200 downregulated overlapping DEGs were identified in both sPNET vs fetal brain and sPNET vs adult brain. The genes involved in the regulatory network upon overlapping DEGs and the TFs were correlated with calcium signaling pathway.
Conclusion: Calcium signaling pathway and several genes (CDK1, CDC20, BUB1B, and BUB1) may play important roles in the pathogenesis of sPNET.

Keywords: primitive neuroectodermal tumor, microarray analysis, protein-protein interaction, transcription factors

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