Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma
Objective This study was aimed to identify prognostic factors in glioma by analysis of the gene expression and DNA methylation data. MethodsThe RNAseq and DNA methylation data associated with glioma were downloaded from GEO and TCGA databases to analyze the differentially expressed genes (DEGs) and...
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| Format: | Article |
| Language: | English |
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AIMS Press
2020-05-01
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| Series: | Mathematical Biosciences and Engineering |
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| Online Access: | https://www.aimspress.com/article/doi/10.3934/mbe.2020217?viewType=HTML |
| _version_ | 1818891209878274048 |
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| author | Bo Wei Rui Wang Le Wang Chao Du |
| author_facet | Bo Wei Rui Wang Le Wang Chao Du |
| author_sort | Bo Wei |
| collection | DOAJ |
| description | Objective This study was aimed to identify prognostic factors in glioma by analysis of the gene expression and DNA methylation data. MethodsThe RNAseq and DNA methylation data associated with glioma were downloaded from GEO and TCGA databases to analyze the differentially expressed genes (DEGs) and methylated genes between tumor and normal tissues. Function and pathway analyses, co-expression network and survival analysis were performed based on these DEGs. The intersection genes of DEGs and differentially methylated genes were obtained followed by function analysis. Results Total 2190 DEGs were identified between tumor and normal tissues, which were significantly enriched in neuron differentiation associated functions, as well as ribosome pathway. There were 6186 methylation sites (2834 up-regulated and 3352 down-regulated) with significant differences in tumor vs. normal. In the constructed co-expression network, DPP6, MAPK10 and RPL3 were hub genes. Survival analysis of 20 DEGs obtained 18 prognostic genes, among which 9 were differentially methylated, such as LHFPL tetraspan subfamily member 3 (LHFPL3), cadherin 20 (CDH20), complexin 2 (CPLX2), and tenascin R (TNR). The intersection of DEGs and differentially methylated genes (632 genes) were significantly enriched in functions of neuron differentiation. Conclusion DPP6, MAPK10 and RPL3 may play important roles in tumorigenesis of glioma. Additionally, methylation of LHFPL3, CDH20, CPLX2, and TNR may serve as prognostic factors of glioma. |
| first_indexed | 2024-12-19T17:37:11Z |
| format | Article |
| id | doaj.art-0b13e8deec504359ae279a2b2ca753d4 |
| institution | Directory Open Access Journal |
| issn | 1551-0018 |
| language | English |
| last_indexed | 2024-12-19T17:37:11Z |
| publishDate | 2020-05-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | Mathematical Biosciences and Engineering |
| spelling | doaj.art-0b13e8deec504359ae279a2b2ca753d42022-12-21T20:12:18ZengAIMS PressMathematical Biosciences and Engineering1551-00182020-05-011743909392410.3934/mbe.2020217Prognostic factor identification by analysis of the gene expression and DNA methylation data in gliomaBo Wei0Rui Wang1Le Wang2Chao Du31. Department of Neurosurgery, The Third Hospital of Jilin University, Changchun 130033, China2. Departments of Radiology, The Third Hospital of Jilin University, Changchun 130033, China3. Departments of Ophthalmology, The Third Hospital of Jilin University, Changchun 130033, China1. Department of Neurosurgery, The Third Hospital of Jilin University, Changchun 130033, ChinaObjective This study was aimed to identify prognostic factors in glioma by analysis of the gene expression and DNA methylation data. MethodsThe RNAseq and DNA methylation data associated with glioma were downloaded from GEO and TCGA databases to analyze the differentially expressed genes (DEGs) and methylated genes between tumor and normal tissues. Function and pathway analyses, co-expression network and survival analysis were performed based on these DEGs. The intersection genes of DEGs and differentially methylated genes were obtained followed by function analysis. Results Total 2190 DEGs were identified between tumor and normal tissues, which were significantly enriched in neuron differentiation associated functions, as well as ribosome pathway. There were 6186 methylation sites (2834 up-regulated and 3352 down-regulated) with significant differences in tumor vs. normal. In the constructed co-expression network, DPP6, MAPK10 and RPL3 were hub genes. Survival analysis of 20 DEGs obtained 18 prognostic genes, among which 9 were differentially methylated, such as LHFPL tetraspan subfamily member 3 (LHFPL3), cadherin 20 (CDH20), complexin 2 (CPLX2), and tenascin R (TNR). The intersection of DEGs and differentially methylated genes (632 genes) were significantly enriched in functions of neuron differentiation. Conclusion DPP6, MAPK10 and RPL3 may play important roles in tumorigenesis of glioma. Additionally, methylation of LHFPL3, CDH20, CPLX2, and TNR may serve as prognostic factors of glioma.https://www.aimspress.com/article/doi/10.3934/mbe.2020217?viewType=HTMLgliomagenemethylationprognosis |
| spellingShingle | Bo Wei Rui Wang Le Wang Chao Du Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma Mathematical Biosciences and Engineering glioma gene methylation prognosis |
| title | Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma |
| title_full | Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma |
| title_fullStr | Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma |
| title_full_unstemmed | Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma |
| title_short | Prognostic factor identification by analysis of the gene expression and DNA methylation data in glioma |
| title_sort | prognostic factor identification by analysis of the gene expression and dna methylation data in glioma |
| topic | glioma gene methylation prognosis |
| url | https://www.aimspress.com/article/doi/10.3934/mbe.2020217?viewType=HTML |
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