Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus database
Abstract Background Colorectal cancer (CRC) is major cancer-related death. The aim of this study was to identify differentially expressed and differentially methylated genes, contributing to explore the molecular mechanism of CRC. Methods Firstly, the data of gene transcriptome and genome-wide DNA m...
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| Format: | Article |
| Language: | English |
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BMC
2022-02-01
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| Series: | BMC Cancer |
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| Online Access: | https://doi.org/10.1186/s12885-022-09185-0 |
| _version_ | 1798023827105513472 |
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| author | Guanglin Wang Feifei Wang Zesong Meng Na Wang Chaoxi Zhou Juan Zhang Lianmei Zhao Guiying Wang Baoen Shan |
| author_facet | Guanglin Wang Feifei Wang Zesong Meng Na Wang Chaoxi Zhou Juan Zhang Lianmei Zhao Guiying Wang Baoen Shan |
| author_sort | Guanglin Wang |
| collection | DOAJ |
| description | Abstract Background Colorectal cancer (CRC) is major cancer-related death. The aim of this study was to identify differentially expressed and differentially methylated genes, contributing to explore the molecular mechanism of CRC. Methods Firstly, the data of gene transcriptome and genome-wide DNA methylation expression were downloaded from the Gene Expression Omnibus database. Secondly, functional analysis of differentially expressed and differentially methylated genes was performed, followed by protein-protein interaction (PPI) analysis. Thirdly, the Cancer Genome Atlas (TCGA) dataset and in vitro experiment was used to validate the expression of selected differentially expressed and differentially methylated genes. Finally, diagnosis and prognosis analysis of selected differentially expressed and differentially methylated genes was performed. Results Up to 1958 differentially expressed (1025 up-regulated and 993 down-regulated) genes and 858 differentially methylated (800 hypermethylated and 58 hypomethylated) genes were identified. Interestingly, some genes, such as GFRA2 and MDFI, were differentially expressed-methylated genes. Purine metabolism (involved IMPDH1), cell adhesion molecules and PI3K-Akt signaling pathway were significantly enriched signaling pathways. GFRA2, FOXQ1, CDH3, CLDN1, SCGN, BEST4, CXCL12, CA7, SHMT2, TRIP13, MDFI and IMPDH1 had a diagnostic value for CRC. In addition, BEST4, SHMT2 and TRIP13 were significantly associated with patients’ survival. Conclusions The identified altered genes may be involved in tumorigenesis of CRC. In addition, BEST4, SHMT2 and TRIP13 may be considered as diagnosis and prognostic biomarkers for CRC patients. |
| first_indexed | 2024-04-11T17:52:43Z |
| format | Article |
| id | doaj.art-01efde8b5dd14838aa947c20dd95b213 |
| institution | Directory Open Access Journal |
| issn | 1471-2407 |
| language | English |
| last_indexed | 2024-04-11T17:52:43Z |
| publishDate | 2022-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Cancer |
| spelling | doaj.art-01efde8b5dd14838aa947c20dd95b2132022-12-22T04:10:59ZengBMCBMC Cancer1471-24072022-02-0122111310.1186/s12885-022-09185-0Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus databaseGuanglin Wang0Feifei Wang1Zesong Meng2Na Wang3Chaoxi Zhou4Juan Zhang5Lianmei Zhao6Guiying Wang7Baoen Shan8The Second Department of Surgery, The Fourth Hospital of Hebei Medical UniversityThe Second Department of Surgery, The Fourth Hospital of Hebei Medical UniversityThe Second Department of Surgery, The Fourth Hospital of Hebei Medical UniversityInstitute of Tumor, The Fourth Hospital of Hebei Medical UniversityThe Second Department of Surgery, The Fourth Hospital of Hebei Medical UniversityThe Second Department of Surgery, The Fourth Hospital of Hebei Medical UniversityScientific Research Center, The Fourth Hospital of Hebei Medical UniversityThe Second Department of Surgery, The Fourth Hospital of Hebei Medical UniversityScientific Research Center, The Fourth Hospital of Hebei Medical UniversityAbstract Background Colorectal cancer (CRC) is major cancer-related death. The aim of this study was to identify differentially expressed and differentially methylated genes, contributing to explore the molecular mechanism of CRC. Methods Firstly, the data of gene transcriptome and genome-wide DNA methylation expression were downloaded from the Gene Expression Omnibus database. Secondly, functional analysis of differentially expressed and differentially methylated genes was performed, followed by protein-protein interaction (PPI) analysis. Thirdly, the Cancer Genome Atlas (TCGA) dataset and in vitro experiment was used to validate the expression of selected differentially expressed and differentially methylated genes. Finally, diagnosis and prognosis analysis of selected differentially expressed and differentially methylated genes was performed. Results Up to 1958 differentially expressed (1025 up-regulated and 993 down-regulated) genes and 858 differentially methylated (800 hypermethylated and 58 hypomethylated) genes were identified. Interestingly, some genes, such as GFRA2 and MDFI, were differentially expressed-methylated genes. Purine metabolism (involved IMPDH1), cell adhesion molecules and PI3K-Akt signaling pathway were significantly enriched signaling pathways. GFRA2, FOXQ1, CDH3, CLDN1, SCGN, BEST4, CXCL12, CA7, SHMT2, TRIP13, MDFI and IMPDH1 had a diagnostic value for CRC. In addition, BEST4, SHMT2 and TRIP13 were significantly associated with patients’ survival. Conclusions The identified altered genes may be involved in tumorigenesis of CRC. In addition, BEST4, SHMT2 and TRIP13 may be considered as diagnosis and prognostic biomarkers for CRC patients.https://doi.org/10.1186/s12885-022-09185-0Colorectal cancerDifferentially expressed genesDifferentially methylated genesDiagnosisPrognosis |
| spellingShingle | Guanglin Wang Feifei Wang Zesong Meng Na Wang Chaoxi Zhou Juan Zhang Lianmei Zhao Guiying Wang Baoen Shan Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus database BMC Cancer Colorectal cancer Differentially expressed genes Differentially methylated genes Diagnosis Prognosis |
| title | Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus database |
| title_full | Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus database |
| title_fullStr | Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus database |
| title_full_unstemmed | Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus database |
| title_short | Uncovering potential genes in colorectal cancer based on integrated and DNA methylation analysis in the gene expression omnibus database |
| title_sort | uncovering potential genes in colorectal cancer based on integrated and dna methylation analysis in the gene expression omnibus database |
| topic | Colorectal cancer Differentially expressed genes Differentially methylated genes Diagnosis Prognosis |
| url | https://doi.org/10.1186/s12885-022-09185-0 |
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