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Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses

BACKGROUND: Medulloblastoma (MB) is the most common intracranial malignant tumor in children. The genes and pathways involved in the pathogenesis of MB are relatively unknown. We aimed to identify potential biomarkers and small-molecule drugs for MB. METHODS: Gene expression profile data sets were o...

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Autores principales: Liu, Zhendong, Zhang, Ruotian, Sun, Zhenying, Yao, Jiawei, Yao, Penglei, Chen, Xin, Wang, Xinzhuang, Gao, Ming, Wan, Jinzhao, Du, Yiming, Zhao, Shiguang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164431/
https://www.ncbi.nlm.nih.gov/pubmed/32328342
http://dx.doi.org/10.7717/peerj.8670
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author Liu, Zhendong
Zhang, Ruotian
Sun, Zhenying
Yao, Jiawei
Yao, Penglei
Chen, Xin
Wang, Xinzhuang
Gao, Ming
Wan, Jinzhao
Du, Yiming
Zhao, Shiguang
author_facet Liu, Zhendong
Zhang, Ruotian
Sun, Zhenying
Yao, Jiawei
Yao, Penglei
Chen, Xin
Wang, Xinzhuang
Gao, Ming
Wan, Jinzhao
Du, Yiming
Zhao, Shiguang
author_sort Liu, Zhendong
collection PubMed
description BACKGROUND: Medulloblastoma (MB) is the most common intracranial malignant tumor in children. The genes and pathways involved in the pathogenesis of MB are relatively unknown. We aimed to identify potential biomarkers and small-molecule drugs for MB. METHODS: Gene expression profile data sets were obtained from the Gene Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) were identified using the Limma package in R. Functional annotation, and cell signaling pathway analysis of DEGs was carried out using DAVID and Kobas. A protein-protein interaction network was generated using STRING. Potential small-molecule drugs were identified using CMap. RESULT: We identified 104 DEGs (29 upregulated; 75 downregulated). Gene ontology analysis showed enrichment in the mitotic cell cycle, cell cycle, spindle, and DNA binding. Cell signaling pathway analysis identified cell cycle, HIF-1 signaling pathway, and phospholipase D signaling pathway as key pathways. SYN1, CNTN2, FAIM2, MT3, and SH3GL2 were the prominent hub genes and their expression level were verified by RT-qPCR. Vorinostat, resveratrol, trichostatin A, pyrvinium, and prochlorperazine were identified as potential drugs for MB. The five hub genes may be targets for diagnosis and treatment of MB, and the small-molecule compounds are promising drugs for effective treatment of MB. CONCLUSION: In this study we obtained five hub genes of MB, SYN1, CNTN2, FAIM2, MT3, and SH3GL2 were confirmed as hub genes. Meanwhile, Vorinostat, resveratrol, trichostatin A, pyrvinium, and prochlorperazine were identified as potential drugs for MB.
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spelling pubmed-71644312020-04-23 Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses Liu, Zhendong Zhang, Ruotian Sun, Zhenying Yao, Jiawei Yao, Penglei Chen, Xin Wang, Xinzhuang Gao, Ming Wan, Jinzhao Du, Yiming Zhao, Shiguang PeerJ Biochemistry BACKGROUND: Medulloblastoma (MB) is the most common intracranial malignant tumor in children. The genes and pathways involved in the pathogenesis of MB are relatively unknown. We aimed to identify potential biomarkers and small-molecule drugs for MB. METHODS: Gene expression profile data sets were obtained from the Gene Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) were identified using the Limma package in R. Functional annotation, and cell signaling pathway analysis of DEGs was carried out using DAVID and Kobas. A protein-protein interaction network was generated using STRING. Potential small-molecule drugs were identified using CMap. RESULT: We identified 104 DEGs (29 upregulated; 75 downregulated). Gene ontology analysis showed enrichment in the mitotic cell cycle, cell cycle, spindle, and DNA binding. Cell signaling pathway analysis identified cell cycle, HIF-1 signaling pathway, and phospholipase D signaling pathway as key pathways. SYN1, CNTN2, FAIM2, MT3, and SH3GL2 were the prominent hub genes and their expression level were verified by RT-qPCR. Vorinostat, resveratrol, trichostatin A, pyrvinium, and prochlorperazine were identified as potential drugs for MB. The five hub genes may be targets for diagnosis and treatment of MB, and the small-molecule compounds are promising drugs for effective treatment of MB. CONCLUSION: In this study we obtained five hub genes of MB, SYN1, CNTN2, FAIM2, MT3, and SH3GL2 were confirmed as hub genes. Meanwhile, Vorinostat, resveratrol, trichostatin A, pyrvinium, and prochlorperazine were identified as potential drugs for MB. PeerJ Inc. 2020-04-14 /pmc/articles/PMC7164431/ /pubmed/32328342 http://dx.doi.org/10.7717/peerj.8670 Text en ©2020 Liu et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Biochemistry
Liu, Zhendong
Zhang, Ruotian
Sun, Zhenying
Yao, Jiawei
Yao, Penglei
Chen, Xin
Wang, Xinzhuang
Gao, Ming
Wan, Jinzhao
Du, Yiming
Zhao, Shiguang
Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses
title Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses
title_full Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses
title_fullStr Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses
title_full_unstemmed Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses
title_short Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses
title_sort identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses
topic Biochemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164431/
https://www.ncbi.nlm.nih.gov/pubmed/32328342
http://dx.doi.org/10.7717/peerj.8670
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