Gene expression network analysis identified CDK1 and KIF11 as possible key molecules in the development of colorectal cancer from normal tissues
Abstract Background Colorectal cancer (CRC) is one of the most common malignancies and the second most common cause of cancer-related mortality worldwide. Despite extensive research, the mechanism underlying CRC development remains unclear. This study aimed to understand the development and progress...
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BioMed Central
2025-06-01
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| Series: | Genomics & Informatics |
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| Online Access: | https://doi.org/10.1186/s44342-025-00046-3 |
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| author | Soo Bin Lee Young Seon Noh Ji-Wook Moon Soohyun Sim Sung Won Han Eun Sun Kim Ji-Yun Lee |
| author_facet | Soo Bin Lee Young Seon Noh Ji-Wook Moon Soohyun Sim Sung Won Han Eun Sun Kim Ji-Yun Lee |
| author_sort | Soo Bin Lee |
| collection | DOAJ |
| description | Abstract Background Colorectal cancer (CRC) is one of the most common malignancies and the second most common cause of cancer-related mortality worldwide. Despite extensive research, the mechanism underlying CRC development remains unclear. This study aimed to understand the development and progression of CRC. Methods Gene network analysis of tumors with their paired normal tissues was performed using the differentially expressed genes dataset for CRC from the Cancer Genome Atlas. Further investigation of the regulatory relationship between hub genes and tumor development was conducted by protein–protein interaction network, Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes pathway analyses using the selected hub genes. Results The network was more centered, and a common hub as well as a hub of hub genes were more connected to each other in the tumor than in the normal tissue, indicating changes in the network from normal to tumor. Eight downregulated and two upregulated hub genes (CDK1 and KIF11) in the tumor were identified. Further, the regulatory pathway was altered, especially in cell cycle and cell division. All R implementation codes are available on the journal website as supplementary materials. Conclusions Our findings may help understand the biological processes underlying tumor development and progression and suggest CDK1 and KIF11 as possible key molecules in the development of CRC. |
| format | Article |
| id | doaj-art-6c3e5b19dcf24d53938b3f829d55ec5d |
| institution | DOAJ |
| issn | 2234-0742 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-6c3e5b19dcf24d53938b3f829d55ec5d2025-08-20T03:10:28ZengBioMed CentralGenomics & Informatics2234-07422025-06-0123111310.1186/s44342-025-00046-3Gene expression network analysis identified CDK1 and KIF11 as possible key molecules in the development of colorectal cancer from normal tissuesSoo Bin Lee0Young Seon Noh1Ji-Wook Moon2Soohyun Sim3Sung Won Han4Eun Sun Kim5Ji-Yun Lee6School of Industrial and Management Engineering, Korea UniversitySchool of Industrial and Management Engineering, Korea UniversityBK21Plus Medical Science, Department of Anatomy, Korea University College of MedicineDepartment of Biomedical Science, Korea University College of MedicineSchool of Industrial and Management Engineering, Korea UniversityDepartment of Internal Medicine, Korea University College of MedicineDepartment of Pathology, Korea University College of MedicineAbstract Background Colorectal cancer (CRC) is one of the most common malignancies and the second most common cause of cancer-related mortality worldwide. Despite extensive research, the mechanism underlying CRC development remains unclear. This study aimed to understand the development and progression of CRC. Methods Gene network analysis of tumors with their paired normal tissues was performed using the differentially expressed genes dataset for CRC from the Cancer Genome Atlas. Further investigation of the regulatory relationship between hub genes and tumor development was conducted by protein–protein interaction network, Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes pathway analyses using the selected hub genes. Results The network was more centered, and a common hub as well as a hub of hub genes were more connected to each other in the tumor than in the normal tissue, indicating changes in the network from normal to tumor. Eight downregulated and two upregulated hub genes (CDK1 and KIF11) in the tumor were identified. Further, the regulatory pathway was altered, especially in cell cycle and cell division. All R implementation codes are available on the journal website as supplementary materials. Conclusions Our findings may help understand the biological processes underlying tumor development and progression and suggest CDK1 and KIF11 as possible key molecules in the development of CRC.https://doi.org/10.1186/s44342-025-00046-3Colorectal cancerNetwork analysisCDK1KIF11 |
| spellingShingle | Soo Bin Lee Young Seon Noh Ji-Wook Moon Soohyun Sim Sung Won Han Eun Sun Kim Ji-Yun Lee Gene expression network analysis identified CDK1 and KIF11 as possible key molecules in the development of colorectal cancer from normal tissues Genomics & Informatics Colorectal cancer Network analysis CDK1 KIF11 |
| title | Gene expression network analysis identified CDK1 and KIF11 as possible key molecules in the development of colorectal cancer from normal tissues |
| title_full | Gene expression network analysis identified CDK1 and KIF11 as possible key molecules in the development of colorectal cancer from normal tissues |
| title_fullStr | Gene expression network analysis identified CDK1 and KIF11 as possible key molecules in the development of colorectal cancer from normal tissues |
| title_full_unstemmed | Gene expression network analysis identified CDK1 and KIF11 as possible key molecules in the development of colorectal cancer from normal tissues |
| title_short | Gene expression network analysis identified CDK1 and KIF11 as possible key molecules in the development of colorectal cancer from normal tissues |
| title_sort | gene expression network analysis identified cdk1 and kif11 as possible key molecules in the development of colorectal cancer from normal tissues |
| topic | Colorectal cancer Network analysis CDK1 KIF11 |
| url | https://doi.org/10.1186/s44342-025-00046-3 |
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