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. 2020 Feb 5:2020:3876834.
doi: 10.1155/2020/3876834. eCollection 2020.

Identification of Genes Associated with the Metastasis of Pheochromocytoma/Paraganglioma Based on Weighted Gene Coexpression Network Analysis

Qisheng Su  1 , Qinpei Ding  2 , Zunni Zhang  1 , Zheng Yang  1 , Yuling Qiu  1 , Xiaohong Li  1 , Wuning Mo  1
Affiliations

Identification of Genes Associated with the Metastasis of Pheochromocytoma/Paraganglioma Based on Weighted Gene Coexpression Network Analysis

Qisheng Su et al. Biomed Res Int. .

Abstract

Background: Pheochromocytoma/paraganglioma (PCPG) is a benign neuroendocrine neoplasm in most cases, but metastasis and other malignant behaviors can be observed in this tumor. The aim of this study was to identify genes associated with the metastasis of PCPG.

Methods: The Cancer Genome Atlas (TCGA) expression profile data and clinical information were downloaded from the cbioportal, and the weighted gene coexpression network analysis (WGCNA) was conducted. The gene coexpression modules were extracted from the network through the WGCNA package of R software. We further extracted metastasis-related modules of PCPG. Enrichment analysis of Biological Process of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes was carried out for important modules, and survival analysis of hub genes in the modules was performed.

Results: A total of 168 PCPG samples were included in this study. The weighted gene coexpression network was constructed with 5125 genes of the top 25% variance among the 20501 genes obtained from the database. We identified 11 coexpression modules, among which the salmon module was associated with the age of PCPG patients at diagnosis, metastasis, and malignancy of the tumors.

Conclusion: WGCNA was performed to identify the gene coexpression modules and hub genes in the metastasis-related gene module of PCPG. The findings in this study provide a new clue for further study of the mechanisms underlying the PCPG metastasis.

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Conflict of interest statement

The authors declare that there are no conflicts of interest regarding the publication of this article.

Figures

Figure 1
Figure 1
Gene coexpression module analysis. (a) Sample dendrogram and trait heatmap. (b) Gene dendrogram and identified coexpression modules.
Figure 2
Figure 2
Module-trait relationships. ME means the module eigengene. Red blocks and green ones indicated positive correlation and negative correlation between ME and the trait, respectively. Color depth was proportional to the absolute value of correlation coefficient (the upper number and lower number in each color block represented the Pearson correlation coefficient and P value, respectively).
Figure 3
Figure 3
Biological processes of Gene Ontology (a) and Kyoto Encyclopedia of Genes and Genomes enrichment analysis based on Webgestalt (b).
Figure 4
Figure 4
Gene coexpression network of the salmon module. The size and color intensity in each circle were proportional to the absolute value of module membership (MM).
Figure 5
Figure 5
Survival analysis of hub genes in the salmon module for PCPG patients.
See this image and copyright information in PMC

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