Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis
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RESEARCH ARTICLE
Open Access
Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis Wenxing Su1,2†, Yi Guan3†, Biao Huang2,4†, Juanjuan Wang1, Yuqian Wei1, Ying Zhao1, Qingqing Jiao5*, Jiang Ji1*, Daojiang Yu6* and Longjiang Xu7
Abstract Background: Melanoma has the highest mortality rate of all skin tumors, and metastases are the major cause of death from it. The molecular mechanism leading to melanoma metastasis is currently unclear. Methods: With the goal of revealing the underlying mechanism, three data sets with accession numbers GSE8401, GSE46517 and GSE7956 were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the differentially expressed gene (DEG) of primary melanoma and metastatic melanoma, three kinds of analyses were performed, namely functional annotation, protein-protein interaction (PPI) network and module construction, and co-expression and drug-gene interaction prediction analysis. Results: A total of 41 up-regulated genes and 79 down-regulated genes was selected for subsequent analyses. Results of pathway enrichment analysis showed that extracellular matrix organization and proteoglycans in cancer are closely related to melanoma metastasis. In addition, seven pivotal genes were identified from PPI network, including CXCL8, THBS1, COL3A1, TIMP3, KIT, DCN, and IGFBP5, which have all been verified in the TCGA database and clinical specimens, but only CXCL8, THBS1 and KIT had significant differences in expression. Conclusions: To conclude, CXCL8, THBS1 and KIT may be the hub genes in the metastasis of melanoma and thus may be regarded as therapeutic targets in the future. Keywords: Melanoma metastasis, Bioinformatic analysis, Differentially expressed genes, Biomarker
* Correspondence: [email protected]; [email protected]; [email protected] † Wenxing Su, Yi Guan and Biao Huang contributed equally to this work. 5 Department of Dermatology, The First Affiliated Hospital of Soochow University, No. 188 Shizi Street, Suzhou, Jiangsu 215000, People’s Republic of China 1 Department of Dermatology, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, Jiangsu 215000, People’s Republic of China 6 Department of Plastic Surgery, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Street, Suzhou, Jiangsu 215000, People’s Republic of China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the a
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