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Common Nevus and Skin Cutaneous Melanoma: Prognostic Genes Identified by Gene Co-Expression Network Analysis

by Lingge Yang 1,2, Yu Xu 1,2, Yan Yan 1,2, Peng Luo 1,2, Shiqi Chen 1,2, Biqiang Zheng 1,2, Wangjun Yan 1,2, Yong Chen 1,2 and Chunmeng Wang 1,2,*
1
Department of Musculoskeletal Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
2
Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
*
Author to whom correspondence should be addressed.
Genes 2019, 10(10), 747; https://doi.org/10.3390/genes10100747
Received: 17 July 2019 / Revised: 30 August 2019 / Accepted: 17 September 2019 / Published: 25 September 2019
(This article belongs to the Section Human Genomics and Genetic Diseases)
Skin cutaneous melanoma (SCM) is a common malignant tumor of the skin and its pathogenesis still needs to be studied. In this work, we constructed a co-expression network and screened for hub genes by weighted gene co-expression network analysis (WGCNA) using the GSE98394 dataset. The relationship between the mRNA expression of hub genes and the prognosis of patients with melanoma was validated by Gene Expression Profiling Interactive Analysis (GEPIA) database. Furthermore, immunohistochemistry in the Human Protein Atlas was used to validate hub genes and grayscale analysis was performed using ImageJ software. It was found that the yellow module was most significantly associated with the difference between common nevus and SCM, and 13 genes whose expression correlation >0.9 were candidate hub genes. The expression of three genes (STK26, KCNT2, CASP12) was correlated with the prognosis of SCM. STK26 (P = 0.0024) and KCNT2 (P < 0.0001) were significantly different between normal skin and SCM. These three hub genes have potential value as predictors for accurate diagnosis and prognosis of SCM in the future. View Full-Text
Keywords: skin cutaneous melanoma; common nevus; GSE98394; weighted gene co-expression network analysis (WGCNA); prognostic genes skin cutaneous melanoma; common nevus; GSE98394; weighted gene co-expression network analysis (WGCNA); prognostic genes
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Yang, L.; Xu, Y.; Yan, Y.; Luo, P.; Chen, S.; Zheng, B.; Yan, W.; Chen, Y.; Wang, C. Common Nevus and Skin Cutaneous Melanoma: Prognostic Genes Identified by Gene Co-Expression Network Analysis. Genes 2019, 10, 747.

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