Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer
Abstract Background Methylation plays an important role in the etiology and pathogenesis of colorectal cancer (CRC). This study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) and pathways in CRC by comprehensive bioinformatics analysis. Methods Data of gene expression...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-08-01
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| Series: | Cancer Cell International |
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| Online Access: | http://link.springer.com/article/10.1186/s12935-017-0444-4 |
| _version_ | 1818477143132209152 |
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| author | Jingwei Liu Hao Li Liping Sun Zhenning Wang Chengzhong Xing Yuan Yuan |
| author_facet | Jingwei Liu Hao Li Liping Sun Zhenning Wang Chengzhong Xing Yuan Yuan |
| author_sort | Jingwei Liu |
| collection | DOAJ |
| description | Abstract Background Methylation plays an important role in the etiology and pathogenesis of colorectal cancer (CRC). This study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) and pathways in CRC by comprehensive bioinformatics analysis. Methods Data of gene expression microarrays (GSE68468, GSE44076) and gene methylation microarrays (GSE29490, GSE17648) were downloaded from GEO database. Aberrantly methylated-DEGs were obtained by GEO2R. Functional and enrichment analyses of selected genes were performed using DAVID database. Protein–protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. MCODE was used for module analysis of the PPI network. Results Totally 411 hypomethylation-high expression genes were identified, which were enriched in biological processes of response to wounding or inflammation, cell proliferation and adhesion. Pathway enrichment showed cytokine–cytokine receptor interaction, p53 signaling and cell cycle. The top 5 hub genes of PPI network were CAD, CCND1, ATM, RB1 and MET. Additionally, 239 hypermethylation-low expression genes were identified, which demonstrated enrichment in biological processes including cell–cell signaling, nerve impulse transmission, etc. Pathway analysis indicated enrichment in calcium signaling, maturity onset diabetes of the young, cell adhesion molecules, etc. The top 5 hub genes of PPI network were EGFR, ACTA1, SST, ESR1 and DNM2. After validation in TCGA database, most hub genes still remained significant. Conclusion In summary, our study indicated possible aberrantly methylated-differentially expressed genes and pathways in CRC by bioinformatics analysis, which may provide novel insights for unraveling pathogenesis of CRC. Hub genes including CAD, CCND1, ATM, RB1, MET, EGFR, ACTA1, SST, ESR1 and DNM2 might serve as aberrantly methylation-based biomarkers for precise diagnosis and treatment of CRC in the future. |
| first_indexed | 2024-12-10T09:34:24Z |
| format | Article |
| id | doaj.art-06dd243ca8c5439b975286d983c791e4 |
| institution | Directory Open Access Journal |
| issn | 1475-2867 |
| language | English |
| last_indexed | 2024-12-10T09:34:24Z |
| publishDate | 2017-08-01 |
| publisher | BMC |
| record_format | Article |
| series | Cancer Cell International |
| spelling | doaj.art-06dd243ca8c5439b975286d983c791e42022-12-22T01:54:14ZengBMCCancer Cell International1475-28672017-08-0117111010.1186/s12935-017-0444-4Aberrantly methylated-differentially expressed genes and pathways in colorectal cancerJingwei Liu0Hao Li1Liping Sun2Zhenning Wang3Chengzhong Xing4Yuan Yuan5Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education DepartmentTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education DepartmentTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education DepartmentTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education DepartmentTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education DepartmentTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education DepartmentAbstract Background Methylation plays an important role in the etiology and pathogenesis of colorectal cancer (CRC). This study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) and pathways in CRC by comprehensive bioinformatics analysis. Methods Data of gene expression microarrays (GSE68468, GSE44076) and gene methylation microarrays (GSE29490, GSE17648) were downloaded from GEO database. Aberrantly methylated-DEGs were obtained by GEO2R. Functional and enrichment analyses of selected genes were performed using DAVID database. Protein–protein interaction (PPI) network was constructed by STRING and visualized in Cytoscape. MCODE was used for module analysis of the PPI network. Results Totally 411 hypomethylation-high expression genes were identified, which were enriched in biological processes of response to wounding or inflammation, cell proliferation and adhesion. Pathway enrichment showed cytokine–cytokine receptor interaction, p53 signaling and cell cycle. The top 5 hub genes of PPI network were CAD, CCND1, ATM, RB1 and MET. Additionally, 239 hypermethylation-low expression genes were identified, which demonstrated enrichment in biological processes including cell–cell signaling, nerve impulse transmission, etc. Pathway analysis indicated enrichment in calcium signaling, maturity onset diabetes of the young, cell adhesion molecules, etc. The top 5 hub genes of PPI network were EGFR, ACTA1, SST, ESR1 and DNM2. After validation in TCGA database, most hub genes still remained significant. Conclusion In summary, our study indicated possible aberrantly methylated-differentially expressed genes and pathways in CRC by bioinformatics analysis, which may provide novel insights for unraveling pathogenesis of CRC. Hub genes including CAD, CCND1, ATM, RB1, MET, EGFR, ACTA1, SST, ESR1 and DNM2 might serve as aberrantly methylation-based biomarkers for precise diagnosis and treatment of CRC in the future.http://link.springer.com/article/10.1186/s12935-017-0444-4MethylationExpressionBioinformaticsColorectal cancer |
| spellingShingle | Jingwei Liu Hao Li Liping Sun Zhenning Wang Chengzhong Xing Yuan Yuan Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer Cancer Cell International Methylation Expression Bioinformatics Colorectal cancer |
| title | Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer |
| title_full | Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer |
| title_fullStr | Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer |
| title_full_unstemmed | Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer |
| title_short | Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer |
| title_sort | aberrantly methylated differentially expressed genes and pathways in colorectal cancer |
| topic | Methylation Expression Bioinformatics Colorectal cancer |
| url | http://link.springer.com/article/10.1186/s12935-017-0444-4 |
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