Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancer
Abstract Background The pan‐cancer analysis has recently brought us into a novel level of cancer research. Nowadays, the Circular RNAs (circRNAs) is becoming increasingly important in the occurrence and progression of tumors. Nevertheless, the specific expression patterns and functions of circRNAs i...
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| Format: | Article |
| Language: | English |
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Wiley
2020-10-01
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| Series: | Cancer Medicine |
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| Online Access: | https://doi.org/10.1002/cam4.3375 |
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| author | Zhanghan Chen Jie Huang Yanling Feng Zehuan Li Ying Jiang |
| author_facet | Zhanghan Chen Jie Huang Yanling Feng Zehuan Li Ying Jiang |
| author_sort | Zhanghan Chen |
| collection | DOAJ |
| description | Abstract Background The pan‐cancer analysis has recently brought us into a novel level of cancer research. Nowadays, the Circular RNAs (circRNAs) is becoming increasingly important in the occurrence and progression of tumors. Nevertheless, the specific expression patterns and functions of circRNAs in the pan‐cancer remains unclear. Here we aimed to explore the expression patterns and functions of circRNAs in pan‐cancer. Methods We combined our microarray with seven circRNA arrays from the Gene Expression Omnibus (GEO) database and transcriptome profiles were acquired from The Cancer Genome Atlas (TCGA) database. A circRNA‐miRNA‐mRNA network was created and analyzed using multiple bioinformatic approaches including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Search Tool for the Retrieval of Interacting Genes (STRING) database, cytoHubba and MCODE app. Cell function assays including CCK‐8 analysis, colony formation, and transwell assay were used to explore pan‐circRNAs’ functions. Results A panel of 6 circRNAs, 11 miRNAs, and 318 mRNAs was found to be differentially expressed (DE) in pan‐cancer. A circRNA‐miRNA‐mRNA network was also constructed. Then, a circRNA‐miRNA‐hub gene network was created according to 5 pan‐circRNAs, 8 pan‐miRNAs, and 16 pan‐mRNAs. Enrichment analysis pointed out the possible association of DEmRNAs with pan‐cancer is transcriptional misregulation in cancer. Overexpression of hsa_circ_0004639 and silence of hsa_circ_0008310 can inhibit the malignant biological properties of cancer cells. Conclusions Six pan‐circRNAs were discovered and their regulating mechanisms were predicted. Those findings together will give a new insight into pan‐cancer research and present potential therapy targeting as well as promising biomarkers. |
| format | Article |
| id | doaj-art-cab1ce1db52945c4bf28a7f4d47d8f7f |
| institution | DOAJ |
| issn | 2045-7634 |
| language | English |
| publishDate | 2020-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | Cancer Medicine |
| spelling | doaj-art-cab1ce1db52945c4bf28a7f4d47d8f7f2025-08-20T02:50:06ZengWileyCancer Medicine2045-76342020-10-019197279729210.1002/cam4.3375Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancerZhanghan Chen0Jie Huang1Yanling Feng2Zehuan Li3Ying Jiang4Department of General Surgery Zhongshan HospitalFudan University Shanghai ChinaDepartment of General Surgery Zhongshan HospitalFudan University Shanghai ChinaDepartment of Pathology Shanghai Public Health Clinical CenterFudan University Shanghai ChinaDepartment of General Surgery Zhongshan HospitalFudan University Shanghai ChinaDepartment of General Surgery Zhongshan HospitalFudan University Shanghai ChinaAbstract Background The pan‐cancer analysis has recently brought us into a novel level of cancer research. Nowadays, the Circular RNAs (circRNAs) is becoming increasingly important in the occurrence and progression of tumors. Nevertheless, the specific expression patterns and functions of circRNAs in the pan‐cancer remains unclear. Here we aimed to explore the expression patterns and functions of circRNAs in pan‐cancer. Methods We combined our microarray with seven circRNA arrays from the Gene Expression Omnibus (GEO) database and transcriptome profiles were acquired from The Cancer Genome Atlas (TCGA) database. A circRNA‐miRNA‐mRNA network was created and analyzed using multiple bioinformatic approaches including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Search Tool for the Retrieval of Interacting Genes (STRING) database, cytoHubba and MCODE app. Cell function assays including CCK‐8 analysis, colony formation, and transwell assay were used to explore pan‐circRNAs’ functions. Results A panel of 6 circRNAs, 11 miRNAs, and 318 mRNAs was found to be differentially expressed (DE) in pan‐cancer. A circRNA‐miRNA‐mRNA network was also constructed. Then, a circRNA‐miRNA‐hub gene network was created according to 5 pan‐circRNAs, 8 pan‐miRNAs, and 16 pan‐mRNAs. Enrichment analysis pointed out the possible association of DEmRNAs with pan‐cancer is transcriptional misregulation in cancer. Overexpression of hsa_circ_0004639 and silence of hsa_circ_0008310 can inhibit the malignant biological properties of cancer cells. Conclusions Six pan‐circRNAs were discovered and their regulating mechanisms were predicted. Those findings together will give a new insight into pan‐cancer research and present potential therapy targeting as well as promising biomarkers.https://doi.org/10.1002/cam4.3375bioinformatics analysisceRNA networkcircRNApan‐cancer |
| spellingShingle | Zhanghan Chen Jie Huang Yanling Feng Zehuan Li Ying Jiang Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancer Cancer Medicine bioinformatics analysis ceRNA network circRNA pan‐cancer |
| title | Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancer |
| title_full | Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancer |
| title_fullStr | Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancer |
| title_full_unstemmed | Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancer |
| title_short | Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan‐cancer |
| title_sort | screening and bioinformatics analysis of a cerna network based on the circular rnas mirnas and mrnas in pan cancer |
| topic | bioinformatics analysis ceRNA network circRNA pan‐cancer |
| url | https://doi.org/10.1002/cam4.3375 |
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