The miRNA‐mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO
ABSTRACT Background Bioinformatics analysis of hepatocellular carcinoma (HCC) expression profiles can aid in understanding its molecular mechanisms and identifying new targets for diagnosis and treatment. Aim In this study, we analyzed expression profile datasets and miRNA expression profiles relate...
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Wiley
2025-01-01
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| Series: | Cancer Reports |
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| Online Access: | https://doi.org/10.1002/cnr2.70098 |
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| author | Razieh Heidari Vahideh Assadollahi Seyedeh Negar Marashi Fatemeh Elahian Seyed Abbas Mirzaei |
| author_facet | Razieh Heidari Vahideh Assadollahi Seyedeh Negar Marashi Fatemeh Elahian Seyed Abbas Mirzaei |
| author_sort | Razieh Heidari |
| collection | DOAJ |
| description | ABSTRACT Background Bioinformatics analysis of hepatocellular carcinoma (HCC) expression profiles can aid in understanding its molecular mechanisms and identifying new targets for diagnosis and treatment. Aim In this study, we analyzed expression profile datasets and miRNA expression profiles related to HCC from the GEO using R software to detect differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs). Methods and results Common DEGs were identified, and a PPI network was constructed using the STRING database and Cytoscape software to identify hub genes. The reduced levels of tumor suppressor miRNAs or down regulated DEmiRs may be increased levels of oncogenes, the oncomirs or up regulated DEmiRs may be decreased levels of tumor suppressor genes in cancerous cells. According to this strategy, increased and decreased DEGs, also increased and decreased DEmiRs were selected. The multimir package was employed to predict target genes for DEmiRs then DEmiRs‐hub gene network created. We identified approximately 1000 overlapping DEGs and 60 DEmiRs. Hub genes included RRM2, MELK, KIF11, KIF23, NCAPG, DLGAP5, BUB1B, AURKB, CCNB1, KIF20A, CCNA2, TTK, PBK, TOP2A, CDK1, MAD2L1, BIRC5, ASPM, CDCA8, and CENPF, all associated with significantly worse survival in HCC. miR‐224, miR‐24, miR‐182, miRNA‐1‐3p, miR‐30a, miR‐27a, and miR‐214 were identified as important DEmiRs with targeting more than six hub genes. Conclusion Generally, our findings offer insight into the interaction of hub genes and miRNAs in the development of HCC by bioinformatics analysis, information that may prove useful in identifying biomarkers and therapeutic targets in HCC. |
| format | Article |
| id | doaj-art-d8b8512cbfe14f29a53e57efef8f21f6 |
| institution | Kabale University |
| issn | 2573-8348 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Cancer Reports |
| spelling | doaj-art-d8b8512cbfe14f29a53e57efef8f21f62025-01-30T15:46:35ZengWileyCancer Reports2573-83482025-01-0181n/an/a10.1002/cnr2.70098The miRNA‐mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEORazieh Heidari0Vahideh Assadollahi1Seyedeh Negar Marashi2Fatemeh Elahian3Seyed Abbas Mirzaei4Cancer Research Center, Basic Health Sciences Institute Shahrekord University of Medical Sciences Shahrekord IranDepartment of Tissue Engineering & Applied Cell Sciences, School of Advanced Technologies Shahrekord University of Medical Sciences Shahrekord IranDepartment of Medical Biotechnology, School of Advanced Technologies Shahrekord University of Medical Sciences Shahrekord IranDepartment of Medical Biotechnology, School of Advanced Technologies Shahrekord University of Medical Sciences Shahrekord IranDepartment of Medical Biotechnology, School of Advanced Technologies Shahrekord University of Medical Sciences Shahrekord IranABSTRACT Background Bioinformatics analysis of hepatocellular carcinoma (HCC) expression profiles can aid in understanding its molecular mechanisms and identifying new targets for diagnosis and treatment. Aim In this study, we analyzed expression profile datasets and miRNA expression profiles related to HCC from the GEO using R software to detect differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRs). Methods and results Common DEGs were identified, and a PPI network was constructed using the STRING database and Cytoscape software to identify hub genes. The reduced levels of tumor suppressor miRNAs or down regulated DEmiRs may be increased levels of oncogenes, the oncomirs or up regulated DEmiRs may be decreased levels of tumor suppressor genes in cancerous cells. According to this strategy, increased and decreased DEGs, also increased and decreased DEmiRs were selected. The multimir package was employed to predict target genes for DEmiRs then DEmiRs‐hub gene network created. We identified approximately 1000 overlapping DEGs and 60 DEmiRs. Hub genes included RRM2, MELK, KIF11, KIF23, NCAPG, DLGAP5, BUB1B, AURKB, CCNB1, KIF20A, CCNA2, TTK, PBK, TOP2A, CDK1, MAD2L1, BIRC5, ASPM, CDCA8, and CENPF, all associated with significantly worse survival in HCC. miR‐224, miR‐24, miR‐182, miRNA‐1‐3p, miR‐30a, miR‐27a, and miR‐214 were identified as important DEmiRs with targeting more than six hub genes. Conclusion Generally, our findings offer insight into the interaction of hub genes and miRNAs in the development of HCC by bioinformatics analysis, information that may prove useful in identifying biomarkers and therapeutic targets in HCC.https://doi.org/10.1002/cnr2.70098bioinformaticsbiomarkerHCChepatocellular carcinomamicroarraymicroRNA |
| spellingShingle | Razieh Heidari Vahideh Assadollahi Seyedeh Negar Marashi Fatemeh Elahian Seyed Abbas Mirzaei The miRNA‐mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO Cancer Reports bioinformatics biomarker HCC hepatocellular carcinoma microarray microRNA |
| title | The miRNA‐mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO |
| title_full | The miRNA‐mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO |
| title_fullStr | The miRNA‐mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO |
| title_full_unstemmed | The miRNA‐mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO |
| title_short | The miRNA‐mRNA Regulatory Network in Human Hepatocellular Carcinoma by Transcriptomic Analysis From GEO |
| title_sort | mirna mrna regulatory network in human hepatocellular carcinoma by transcriptomic analysis from geo |
| topic | bioinformatics biomarker HCC hepatocellular carcinoma microarray microRNA |
| url | https://doi.org/10.1002/cnr2.70098 |
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