Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach
Abstract In this study, we investigated cancer cellular networks in the context of gene interactions and their associated patterns in order to recognize the structural features underlying this disease. We aim to propose that the quest of understanding cancer takes us beyond pairwise interactions bet...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-94847-5 |
| _version_ | 1818841206102163456 |
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| author | Hosein Masoomy Behrouz Askari Samin Tajik Abbas K. Rizi G. Reza Jafari |
| author_facet | Hosein Masoomy Behrouz Askari Samin Tajik Abbas K. Rizi G. Reza Jafari |
| author_sort | Hosein Masoomy |
| collection | DOAJ |
| description | Abstract In this study, we investigated cancer cellular networks in the context of gene interactions and their associated patterns in order to recognize the structural features underlying this disease. We aim to propose that the quest of understanding cancer takes us beyond pairwise interactions between genes to a higher-order construction. We characterize the most prominent network deviations in the gene interaction patterns between cancer and normal samples that contribute to the complexity of this disease. What we hope is that through understanding these interaction patterns we will notice a deeper structure in the cancer network. This study uncovers the significant deviations that topological features in cancerous cells show from the healthy one, where the last stage of filtration confirms the importance of one-dimensional holes (topological loops) in cancerous cells and two-dimensional holes (topological voids) in healthy cells. In the small threshold region, the drop in the number of connected components of the cancer network, along with the rise in the number of loops and voids, all occurring at some smaller weight values compared to the normal case, reveals the cancerous network tendency to certain pathways. |
| first_indexed | 2024-12-19T04:22:23Z |
| format | Article |
| id | doaj.art-4c30b04e5ac44b70a69771449d5bd380 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-19T04:22:23Z |
| publishDate | 2021-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-4c30b04e5ac44b70a69771449d5bd3802022-12-21T20:36:07ZengNature PortfolioScientific Reports2045-23222021-08-0111111110.1038/s41598-021-94847-5Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approachHosein Masoomy0Behrouz Askari1Samin Tajik2Abbas K. Rizi3G. Reza Jafari4Physics Department, Shahid Beheshti UniversityPhysics Department, Shahid Beheshti UniversityPhysics Department, Brock UniversityDepartment of Computer Science, School of Science, Aalto UniversityPhysics Department, Shahid Beheshti UniversityAbstract In this study, we investigated cancer cellular networks in the context of gene interactions and their associated patterns in order to recognize the structural features underlying this disease. We aim to propose that the quest of understanding cancer takes us beyond pairwise interactions between genes to a higher-order construction. We characterize the most prominent network deviations in the gene interaction patterns between cancer and normal samples that contribute to the complexity of this disease. What we hope is that through understanding these interaction patterns we will notice a deeper structure in the cancer network. This study uncovers the significant deviations that topological features in cancerous cells show from the healthy one, where the last stage of filtration confirms the importance of one-dimensional holes (topological loops) in cancerous cells and two-dimensional holes (topological voids) in healthy cells. In the small threshold region, the drop in the number of connected components of the cancer network, along with the rise in the number of loops and voids, all occurring at some smaller weight values compared to the normal case, reveals the cancerous network tendency to certain pathways.https://doi.org/10.1038/s41598-021-94847-5 |
| spellingShingle | Hosein Masoomy Behrouz Askari Samin Tajik Abbas K. Rizi G. Reza Jafari Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach Scientific Reports |
| title | Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach |
| title_full | Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach |
| title_fullStr | Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach |
| title_full_unstemmed | Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach |
| title_short | Topological analysis of interaction patterns in cancer-specific gene regulatory network: persistent homology approach |
| title_sort | topological analysis of interaction patterns in cancer specific gene regulatory network persistent homology approach |
| url | https://doi.org/10.1038/s41598-021-94847-5 |
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