Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular Carcinoma
Disulfidptosis is a newly discovered cellular programmed cell death mode. Presently, a considerable number of genes related to disulfidptosis remain undiscovered, and its significance in hepatocellular carcinoma remains unrevealed. We have developed a powerful analytical method called RF-GSEA for id...
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| Format: | Article |
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MDPI AG
2023-11-01
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| Series: | Current Issues in Molecular Biology |
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| Online Access: | https://www.mdpi.com/1467-3045/45/12/593 |
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| author | Linghao Ni Qian Yu Ruijia You Chen Chen Bin Peng |
| author_facet | Linghao Ni Qian Yu Ruijia You Chen Chen Bin Peng |
| author_sort | Linghao Ni |
| collection | DOAJ |
| description | Disulfidptosis is a newly discovered cellular programmed cell death mode. Presently, a considerable number of genes related to disulfidptosis remain undiscovered, and its significance in hepatocellular carcinoma remains unrevealed. We have developed a powerful analytical method called RF-GSEA for identifying potential genes associated with disulfidptosis. This method draws inspiration from gene regulation networks and graph theory, and it is implemented through a combination of random forest regression model and Gene Set Enrichment Analysis. Subsequently, to validate the practical application value of this method, we applied it to hepatocellular carcinoma. Based on the RF-GSEA method, we developed a disulfidptosis-related signature. Lastly, we looked into how the disulfidptosis-related signature is connected to HCC prognosis, the tumor microenvironment, the effectiveness of immunotherapy, and the sensitivity of chemotherapy drugs. The RF-GSEA method identified a total of 220 disulfidptosis-related genes, from which 7 were selected to construct the disulfidptosis-related signature. The high-disulfidptosis-related score group had a worse prognosis compared to the low-disulfidptosis-related score group and showed lower infiltration levels of immune-promoting cells. The high-disulfidptosis-related score group had a higher likelihood of benefiting from immunotherapy compared to the low-disulfidptosis-related score group. The RF-GSEA method is a powerful tool for identifying disulfidptosis-related genes. The disulfidptosis-related signature effectively predicts HCC prognosis, immunotherapy response, and drug sensitivity. |
| first_indexed | 2024-03-08T20:54:04Z |
| format | Article |
| id | doaj.art-c54ba86373b64db5a06dd888169d776f |
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| issn | 1467-3037 1467-3045 |
| language | English |
| last_indexed | 2024-03-08T20:54:04Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
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| series | Current Issues in Molecular Biology |
| spelling | doaj.art-c54ba86373b64db5a06dd888169d776f2023-12-22T14:00:36ZengMDPI AGCurrent Issues in Molecular Biology1467-30371467-30452023-11-0145129450947010.3390/cimb45120593Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular CarcinomaLinghao Ni0Qian Yu1Ruijia You2Chen Chen3Bin Peng4School of Public Health, Chongqing Medical University, Chongqing 400016, ChinaSchool of Public Health, Chongqing Medical University, Chongqing 400016, ChinaSchool of Public Health, Chongqing Medical University, Chongqing 400016, ChinaSchool of Public Health, Chongqing Medical University, Chongqing 400016, ChinaSchool of Public Health, Chongqing Medical University, Chongqing 400016, ChinaDisulfidptosis is a newly discovered cellular programmed cell death mode. Presently, a considerable number of genes related to disulfidptosis remain undiscovered, and its significance in hepatocellular carcinoma remains unrevealed. We have developed a powerful analytical method called RF-GSEA for identifying potential genes associated with disulfidptosis. This method draws inspiration from gene regulation networks and graph theory, and it is implemented through a combination of random forest regression model and Gene Set Enrichment Analysis. Subsequently, to validate the practical application value of this method, we applied it to hepatocellular carcinoma. Based on the RF-GSEA method, we developed a disulfidptosis-related signature. Lastly, we looked into how the disulfidptosis-related signature is connected to HCC prognosis, the tumor microenvironment, the effectiveness of immunotherapy, and the sensitivity of chemotherapy drugs. The RF-GSEA method identified a total of 220 disulfidptosis-related genes, from which 7 were selected to construct the disulfidptosis-related signature. The high-disulfidptosis-related score group had a worse prognosis compared to the low-disulfidptosis-related score group and showed lower infiltration levels of immune-promoting cells. The high-disulfidptosis-related score group had a higher likelihood of benefiting from immunotherapy compared to the low-disulfidptosis-related score group. The RF-GSEA method is a powerful tool for identifying disulfidptosis-related genes. The disulfidptosis-related signature effectively predicts HCC prognosis, immunotherapy response, and drug sensitivity.https://www.mdpi.com/1467-3045/45/12/593disulfidptosisrandom forest regression modelhepatocellular carcinoma |
| spellingShingle | Linghao Ni Qian Yu Ruijia You Chen Chen Bin Peng Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular Carcinoma Current Issues in Molecular Biology disulfidptosis random forest regression model hepatocellular carcinoma |
| title | Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular Carcinoma |
| title_full | Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular Carcinoma |
| title_fullStr | Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular Carcinoma |
| title_full_unstemmed | Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular Carcinoma |
| title_short | Development of the RF-GSEA Method for Identifying Disulfidptosis-Related Genes and Application in Hepatocellular Carcinoma |
| title_sort | development of the rf gsea method for identifying disulfidptosis related genes and application in hepatocellular carcinoma |
| topic | disulfidptosis random forest regression model hepatocellular carcinoma |
| url | https://www.mdpi.com/1467-3045/45/12/593 |
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