Identification of Cancer Hallmarks Based on the Gene Co-expression Networks of Seven Cancers
Identifying the hallmarks of cancer is essential for cancer research, and the genes involved in cancer hallmarks are likely to be cancer drivers. However, there is no appropriate method in the current literature for identifying genetic cancer hallmarks, especially considering the interrelationships...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-02-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.00099/full |
| _version_ | 1818140745186410496 |
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| author | Ling-Hao Yu Qin-Wei Huang Xiong-Hui Zhou |
| author_facet | Ling-Hao Yu Qin-Wei Huang Xiong-Hui Zhou |
| author_sort | Ling-Hao Yu |
| collection | DOAJ |
| description | Identifying the hallmarks of cancer is essential for cancer research, and the genes involved in cancer hallmarks are likely to be cancer drivers. However, there is no appropriate method in the current literature for identifying genetic cancer hallmarks, especially considering the interrelationships among the genes. Here, we hypothesized that “dense clusters” (or “communities”) in the gene co-expression networks of cancer patients may represent functional units regarding cancer formation and progression, and the communities present in the co-expression networks of multiple types of cancer may be cancer hallmarks. Consequently, we mined the conserved communities in the gene co-expression networks of seven cancers in order to identify candidate hallmarks. Functional annotation of the communities showed that they were mainly related to immune response, the cell cycle and the biological processes that maintain basic cellular functions. Survival analysis using the genes involved in the conserved communities verified that two of these hallmarks could predict the survival risks of cancer patients in multiple types of cancer. Furthermore, the genes involved in these hallmarks, one of which was related to the cell cycle, could be useful in screening for cancer drugs. |
| first_indexed | 2024-12-11T10:48:52Z |
| format | Article |
| id | doaj.art-d28db88c5f664728a95e4725d5e134a0 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-11T10:48:52Z |
| publishDate | 2019-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-d28db88c5f664728a95e4725d5e134a02022-12-22T01:10:24ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-02-011010.3389/fgene.2019.00099432458Identification of Cancer Hallmarks Based on the Gene Co-expression Networks of Seven CancersLing-Hao Yu0Qin-Wei Huang1Xiong-Hui Zhou2College of Science, Huazhong Agricultural University, Wuhan, ChinaCollege of Science, Huazhong Agricultural University, Wuhan, ChinaHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, ChinaIdentifying the hallmarks of cancer is essential for cancer research, and the genes involved in cancer hallmarks are likely to be cancer drivers. However, there is no appropriate method in the current literature for identifying genetic cancer hallmarks, especially considering the interrelationships among the genes. Here, we hypothesized that “dense clusters” (or “communities”) in the gene co-expression networks of cancer patients may represent functional units regarding cancer formation and progression, and the communities present in the co-expression networks of multiple types of cancer may be cancer hallmarks. Consequently, we mined the conserved communities in the gene co-expression networks of seven cancers in order to identify candidate hallmarks. Functional annotation of the communities showed that they were mainly related to immune response, the cell cycle and the biological processes that maintain basic cellular functions. Survival analysis using the genes involved in the conserved communities verified that two of these hallmarks could predict the survival risks of cancer patients in multiple types of cancer. Furthermore, the genes involved in these hallmarks, one of which was related to the cell cycle, could be useful in screening for cancer drugs.https://www.frontiersin.org/article/10.3389/fgene.2019.00099/fullcancer hallmarksgene co-expression networkcancer prognosispan-cancer analysisdrug target |
| spellingShingle | Ling-Hao Yu Qin-Wei Huang Xiong-Hui Zhou Identification of Cancer Hallmarks Based on the Gene Co-expression Networks of Seven Cancers Frontiers in Genetics cancer hallmarks gene co-expression network cancer prognosis pan-cancer analysis drug target |
| title | Identification of Cancer Hallmarks Based on the Gene Co-expression Networks of Seven Cancers |
| title_full | Identification of Cancer Hallmarks Based on the Gene Co-expression Networks of Seven Cancers |
| title_fullStr | Identification of Cancer Hallmarks Based on the Gene Co-expression Networks of Seven Cancers |
| title_full_unstemmed | Identification of Cancer Hallmarks Based on the Gene Co-expression Networks of Seven Cancers |
| title_short | Identification of Cancer Hallmarks Based on the Gene Co-expression Networks of Seven Cancers |
| title_sort | identification of cancer hallmarks based on the gene co expression networks of seven cancers |
| topic | cancer hallmarks gene co-expression network cancer prognosis pan-cancer analysis drug target |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.00099/full |
| work_keys_str_mv | AT linghaoyu identificationofcancerhallmarksbasedonthegenecoexpressionnetworksofsevencancers AT qinweihuang identificationofcancerhallmarksbasedonthegenecoexpressionnetworksofsevencancers AT xionghuizhou identificationofcancerhallmarksbasedonthegenecoexpressionnetworksofsevencancers |