A network view of human immune system and virus-human interaction
The immune system is highly networked and complex, which is continuously changing as encountering old and new pathogens. However, reductionism-based researches do not give a systematic understanding of the molecular mechanism of the immune response and viral pathogenesis. Here, we present HUMPPI-202...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.997851/full |
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| author | Kang Tang Kang Tang Jing Tang Jing Tang Jinfeng Zeng Jinfeng Zeng Wei Shen Wei Shen Min Zou Min Zou Chi Zhang Chi Zhang Qianru Sun Qianru Sun Xiaoyan Ye Chunwei Li Caijun Sun Caijun Sun Siyang Liu Siyang Liu Guozhi Jiang Guozhi Jiang Xiangjun Du Xiangjun Du Xiangjun Du |
| author_facet | Kang Tang Kang Tang Jing Tang Jing Tang Jinfeng Zeng Jinfeng Zeng Wei Shen Wei Shen Min Zou Min Zou Chi Zhang Chi Zhang Qianru Sun Qianru Sun Xiaoyan Ye Chunwei Li Caijun Sun Caijun Sun Siyang Liu Siyang Liu Guozhi Jiang Guozhi Jiang Xiangjun Du Xiangjun Du Xiangjun Du |
| author_sort | Kang Tang |
| collection | DOAJ |
| description | The immune system is highly networked and complex, which is continuously changing as encountering old and new pathogens. However, reductionism-based researches do not give a systematic understanding of the molecular mechanism of the immune response and viral pathogenesis. Here, we present HUMPPI-2022, a high-quality human protein-protein interaction (PPI) network, containing > 11,000 protein-coding genes with > 78,000 interactions. The network topology and functional characteristics analyses of the immune-related genes (IRGs) reveal that IRGs are mostly located in the center of the network and link genes of diverse biological processes, which may reflect the gene pleiotropy phenomenon. Moreover, the virus-human interactions reveal that pan-viral targets are mostly hubs, located in the center of the network and enriched in fundamental biological processes, but not for coronavirus. Finally, gene age effect was analyzed from the view of the host network for IRGs and virally-targeted genes (VTGs) during evolution, with IRGs gradually became hubs and integrated into host network through bridging functionally differentiated modules. Briefly, HUMPPI-2022 serves as a valuable resource for gaining a better understanding of the composition and evolution of human immune system, as well as the pathogenesis of viruses. |
| first_indexed | 2024-04-12T11:41:26Z |
| format | Article |
| id | doaj.art-02a0ec95ad5e464aa322bda1123f8700 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-12T11:41:26Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-02a0ec95ad5e464aa322bda1123f87002022-12-22T03:34:35ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-10-011310.3389/fimmu.2022.997851997851A network view of human immune system and virus-human interactionKang Tang0Kang Tang1Jing Tang2Jing Tang3Jinfeng Zeng4Jinfeng Zeng5Wei Shen6Wei Shen7Min Zou8Min Zou9Chi Zhang10Chi Zhang11Qianru Sun12Qianru Sun13Xiaoyan Ye14Chunwei Li15Caijun Sun16Caijun Sun17Siyang Liu18Siyang Liu19Guozhi Jiang20Guozhi Jiang21Xiangjun Du22Xiangjun Du23Xiangjun Du24School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaDepartment of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaDepartment of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, ChinaDepartment of Otolaryngology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaSchool of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, ChinaSchool of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, ChinaKey Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, ChinaThe immune system is highly networked and complex, which is continuously changing as encountering old and new pathogens. However, reductionism-based researches do not give a systematic understanding of the molecular mechanism of the immune response and viral pathogenesis. Here, we present HUMPPI-2022, a high-quality human protein-protein interaction (PPI) network, containing > 11,000 protein-coding genes with > 78,000 interactions. The network topology and functional characteristics analyses of the immune-related genes (IRGs) reveal that IRGs are mostly located in the center of the network and link genes of diverse biological processes, which may reflect the gene pleiotropy phenomenon. Moreover, the virus-human interactions reveal that pan-viral targets are mostly hubs, located in the center of the network and enriched in fundamental biological processes, but not for coronavirus. Finally, gene age effect was analyzed from the view of the host network for IRGs and virally-targeted genes (VTGs) during evolution, with IRGs gradually became hubs and integrated into host network through bridging functionally differentiated modules. Briefly, HUMPPI-2022 serves as a valuable resource for gaining a better understanding of the composition and evolution of human immune system, as well as the pathogenesis of viruses.https://www.frontiersin.org/articles/10.3389/fimmu.2022.997851/fullprotein-protein interactiongene moduleimmune-related genevirus-human interactionnew gene |
| spellingShingle | Kang Tang Kang Tang Jing Tang Jing Tang Jinfeng Zeng Jinfeng Zeng Wei Shen Wei Shen Min Zou Min Zou Chi Zhang Chi Zhang Qianru Sun Qianru Sun Xiaoyan Ye Chunwei Li Caijun Sun Caijun Sun Siyang Liu Siyang Liu Guozhi Jiang Guozhi Jiang Xiangjun Du Xiangjun Du Xiangjun Du A network view of human immune system and virus-human interaction Frontiers in Immunology protein-protein interaction gene module immune-related gene virus-human interaction new gene |
| title | A network view of human immune system and virus-human interaction |
| title_full | A network view of human immune system and virus-human interaction |
| title_fullStr | A network view of human immune system and virus-human interaction |
| title_full_unstemmed | A network view of human immune system and virus-human interaction |
| title_short | A network view of human immune system and virus-human interaction |
| title_sort | network view of human immune system and virus human interaction |
| topic | protein-protein interaction gene module immune-related gene virus-human interaction new gene |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.997851/full |
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