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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2020
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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. |
format | Online Article Text |
id | pubmed-7164431 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
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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