Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics
Autoimmune diseases (ADs) are a broad range of diseases in which the immune response to self-antigens causes damage or disorder of tissues, and the genetic susceptibility is regarded as the key etiology of ADs. Accumulating evidence has suggested that there are certain commonalities among different...
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Frontiers Media S.A.
2021-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.758041/full |
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| author | Yanjun Ding Yanjun Ding Mintian Cui Jun Qian Chao Wang Qi Shen Hongbiao Ren Liangshuang Li Fengmin Zhang Ruijie Zhang |
| author_facet | Yanjun Ding Yanjun Ding Mintian Cui Jun Qian Chao Wang Qi Shen Hongbiao Ren Liangshuang Li Fengmin Zhang Ruijie Zhang |
| author_sort | Yanjun Ding |
| collection | DOAJ |
| description | Autoimmune diseases (ADs) are a broad range of diseases in which the immune response to self-antigens causes damage or disorder of tissues, and the genetic susceptibility is regarded as the key etiology of ADs. Accumulating evidence has suggested that there are certain commonalities among different ADs. However, the theoretical research about similarity between ADs is still limited. In this work, we first computed the genetic similarity between 26 ADs based on three measurements: network similarity (NetSim), functional similarity (FunSim), and semantic similarity (SemSim), and systematically identified three significant pairs of similar ADs: rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), myasthenia gravis (MG) and autoimmune thyroiditis (AIT), and autoimmune polyendocrinopathies (AP) and uveomeningoencephalitic syndrome (Vogt-Koyanagi-Harada syndrome, VKH). Then we investigated the gene ontology terms and pathways enriched by the three significant AD pairs through functional analysis. By the cluster analysis on the similarity matrix of 26 ADs, we embedded the three significant AD pairs in three different disease clusters respectively, and the ADs of each disease cluster might have high genetic similarity. We also detected the risk genes in common among the ADs which belonged to the same disease cluster. Overall, our findings will provide significant insight in the commonalities of different ADs in genetics, and contribute to the discovery of novel biomarkers and the development of new therapeutic methods for ADs. |
| first_indexed | 2024-12-19T00:36:12Z |
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| id | doaj.art-1849509947b1413fbf48f440dcfa4f95 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-19T00:36:12Z |
| publishDate | 2021-11-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-1849509947b1413fbf48f440dcfa4f952022-12-21T20:44:45ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-11-011210.3389/fgene.2021.758041758041Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and SemanticsYanjun Ding0Yanjun Ding1Mintian Cui2Jun Qian3Chao Wang4Qi Shen5Hongbiao Ren6Liangshuang Li7Fengmin Zhang8Ruijie Zhang9College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, ChinaDepartment of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin, ChinaCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, ChinaDepartment of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin, ChinaCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, ChinaCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, ChinaCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, ChinaCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, ChinaDepartment of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin, ChinaCollege of Bioinformatics Science and Technology, Harbin Medical University, Harbin, ChinaAutoimmune diseases (ADs) are a broad range of diseases in which the immune response to self-antigens causes damage or disorder of tissues, and the genetic susceptibility is regarded as the key etiology of ADs. Accumulating evidence has suggested that there are certain commonalities among different ADs. However, the theoretical research about similarity between ADs is still limited. In this work, we first computed the genetic similarity between 26 ADs based on three measurements: network similarity (NetSim), functional similarity (FunSim), and semantic similarity (SemSim), and systematically identified three significant pairs of similar ADs: rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), myasthenia gravis (MG) and autoimmune thyroiditis (AIT), and autoimmune polyendocrinopathies (AP) and uveomeningoencephalitic syndrome (Vogt-Koyanagi-Harada syndrome, VKH). Then we investigated the gene ontology terms and pathways enriched by the three significant AD pairs through functional analysis. By the cluster analysis on the similarity matrix of 26 ADs, we embedded the three significant AD pairs in three different disease clusters respectively, and the ADs of each disease cluster might have high genetic similarity. We also detected the risk genes in common among the ADs which belonged to the same disease cluster. Overall, our findings will provide significant insight in the commonalities of different ADs in genetics, and contribute to the discovery of novel biomarkers and the development of new therapeutic methods for ADs.https://www.frontiersin.org/articles/10.3389/fgene.2021.758041/fullADsgenetic susceptibilitynetwork similarityfunctional similaritysemantic similarityautoimmune tautology |
| spellingShingle | Yanjun Ding Yanjun Ding Mintian Cui Jun Qian Chao Wang Qi Shen Hongbiao Ren Liangshuang Li Fengmin Zhang Ruijie Zhang Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics Frontiers in Genetics ADs genetic susceptibility network similarity functional similarity semantic similarity autoimmune tautology |
| title | Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics |
| title_full | Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics |
| title_fullStr | Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics |
| title_full_unstemmed | Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics |
| title_short | Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics |
| title_sort | calculation of similarity between 26 autoimmune diseases based on three measurements including network function and semantics |
| topic | ADs genetic susceptibility network similarity functional similarity semantic similarity autoimmune tautology |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2021.758041/full |
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