{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,8]],"date-time":"2025-12-08T22:00:31Z","timestamp":1765231231276,"version":"3.41.2"},"reference-count":57,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,11,11]],"date-time":"2021-11-11T00:00:00Z","timestamp":1636588800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005046","name":"Natural Science Foundation of Heilongjiang Province","doi-asserted-by":"publisher","award":["LH2019C043"],"award-info":[{"award-number":["LH2019C043"]}],"id":[{"id":"10.13039\/501100005046","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3389\/fgene.2021.758041","type":"journal-article","created":{"date-parts":[[2021,11,11]],"date-time":"2021-11-11T09:48:11Z","timestamp":1636624091000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Calculation of Similarity Between 26 Autoimmune Diseases Based on Three Measurements Including Network, Function, and Semantics"],"prefix":"10.3389","volume":"12","author":[{"given":"Yanjun","family":"Ding","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mintian","family":"Cui","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jun","family":"Qian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chao","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qi","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongbiao","family":"Ren","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liangshuang","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fengmin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruijie","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2021,11,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/j.jaut.2012.05.008","article-title":"Sj\u00f6gren's Syndrome at the Crossroad of Polyautoimmunity","volume":"39","author":"Amador-Patarroyo","year":"2012","journal-title":"J. Autoimmun."},{"key":"B2","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1080\/17402520600876762","article-title":"Is There a Common Genetic Basis for Autoimmune Diseases","volume":"13","author":"Anaya","year":"2006","journal-title":"Clin. Develop. Immunol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.jbspin.2016.11.012","article-title":"The Autoimmune Tautology. A Summary of Evidence","volume":"84","author":"Anaya","year":"2017","journal-title":"Jt. Bone Spine"},{"key":"B4","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1016\/j.autrev.2014.01.049","article-title":"The Diagnosis and Clinical Significance of Polyautoimmunity","volume":"13","author":"Anaya","year":"2014","journal-title":"Autoimmun. Rev."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1574","DOI":"10.1038\/s41590-019-0466-2","article-title":"Interferon Target-Gene Expression and Epigenomic Signatures in Health and Disease","volume":"20","author":"Barrat","year":"2019","journal-title":"Nat. Immunol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1038\/ng0504-431","article-title":"The Genetic Association Database","volume":"36","author":"Becker","year":"2004","journal-title":"Nat. Genet."},{"key":"B7","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1111\/cen.14304","article-title":"Prevalence of Latent and Overt Polyautoimmunity in Autoimmune Thyroid Disease: A Systematic Review and Meta\u2010analysis","volume":"93","author":"Botello","year":"2020","journal-title":"Clin. Endocrinol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1186\/1741-7015-11-73","article-title":"How Do Autoimmune Diseases Cluster in Families? A Systematic Review and Meta-Analysis","volume":"11","author":"C\u00e1rdenas-Rold\u00e1n","year":"2013","journal-title":"BMC Med."},{"key":"B9","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1016\/j.jaci.2009.12.980","article-title":"Overview of the Immune Response","volume":"125","author":"Chaplin","year":"2010","journal-title":"J. Allergy Clin. Immunol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/1752-0509-4-78","article-title":"Network Properties of Human Disease Genes with Pleiotropic Effects","volume":"4","author":"Chavali","year":"2010","journal-title":"BMC Syst. Biol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"e99415","DOI":"10.1371\/journal.pone.0099415","article-title":"SemFunSim: a New Method for Measuring Disease Similarity by Integrating Semantic and Gene Functional Association","volume":"9","author":"Cheng","year":"2014","journal-title":"PLoS ONE"},{"key":"B12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2012\/569728","article-title":"Shared HLA Class II in Six Autoimmune Diseases in Latin America: A Meta-Analysis","volume":"2012","author":"Cruz-Tapias","year":"2012","journal-title":"Autoimmune Dis."},{"key":"B13","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1093\/bib\/bby109","article-title":"Bioinformatics Methodologies for Coeliac Disease and its Comorbidities","volume":"21","author":"Del Prete","year":"2018","journal-title":"Brief. Bioinform."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1769","DOI":"10.1093\/bib\/bby049","article-title":"Disease Classification: from Phenotypic Similarity to Integrative Genomics and beyond","volume":"20","author":"Dozmorov","year":"2019","journal-title":"Brief. Bioinform."},{"key":"B15","doi-asserted-by":"publisher","first-page":"1046","DOI":"10.1210\/clinem\/dgz289","article-title":"Th1 Chemokines in Autoimmune Endocrine Disorders","volume":"105","author":"Fallahi","year":"2020","journal-title":"J. Clin. Endocrinol. Metab."},{"key":"B16","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1146\/annurev.immunol.021908.132653","article-title":"Recent Advances in the Genetics of Autoimmune Disease","volume":"27","author":"Gregersen","year":"2009","journal-title":"Annu. Rev. Immunol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"e1000353","DOI":"10.1371\/journal.pcbi.1000353","article-title":"A Dynamic Network Approach for the Study of Human Phenotypes","volume":"5","author":"Hidalgo","year":"2009","journal-title":"Plos Comput. Biol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"4838","DOI":"10.2741\/3043","article-title":"Recent Acquisitions on the Genetic Basis of Autoimmune Disease","volume":"13","author":"Hill","year":"2008","journal-title":"Front. Biosci."},{"key":"B19","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1016\/j.immuni.2009.09.002","article-title":"Cross-regulation of Signaling Pathways by Interferon-\u03b3: Implications for Immune Responses and Autoimmune Diseases","volume":"31","author":"Hu","year":"2009","journal-title":"Immunity"},{"key":"B20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics Enrichment Tools: Paths toward the Comprehensive Functional Analysis of Large Gene Lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"B21","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1016\/j.jaut.2016.03.003","article-title":"Gender-specific Incidence of Autoimmune Diseases from National Registers","volume":"69","author":"Ji","year":"2016","journal-title":"J. Autoimmun."},{"key":"B22","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1007\/s00251-018-1082-2","article-title":"Genetics of Antigen Processing and Presentation","volume":"71","author":"Kelly","year":"2019","journal-title":"Immunogenetics"},{"key":"B23","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/bs.ircmb.2019.07.005","article-title":"Antigen Processing and Presentation","volume":"348","author":"Kotsias","year":"2019","journal-title":"Int. Rev. Cel Mol. Biol."},{"key":"B24","doi-asserted-by":"publisher","first-page":"e00537","DOI":"10.1002\/brb3.537","article-title":"Prevalence and Impact of Autoimmune Thyroid Disease on Myasthenia Gravis Course","volume":"6","author":"Kubiszewska","year":"2016","journal-title":"Brain Behav."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1109","DOI":"10.1101\/gr.118992.110","article-title":"Prioritizing Candidate Disease Genes by Network-Based Boosting of Genome-wide Association Data","volume":"21","author":"Lee","year":"2011","journal-title":"Genome Res."},{"key":"B26","doi-asserted-by":"publisher","first-page":"460","DOI":"10.3389\/fphar.2017.00460","article-title":"Drugs for Autoimmune Inflammatory Diseases: From Small Molecule Compounds to Anti-TNF Biologics","volume":"8","author":"Li","year":"2017","journal-title":"Front. Pharmacol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"1018","DOI":"10.1038\/nm.3933","article-title":"Meta-analysis of Shared Genetic Architecture across Ten Pediatric Autoimmune Diseases","volume":"21","author":"Li","year":"2015","journal-title":"Nat. Med."},{"key":"B28","doi-asserted-by":"publisher","first-page":"1070","DOI":"10.1136\/annrheumdis-2019-215442","article-title":"T Cell Receptor \u03b2 Repertoires as Novel Diagnostic Markers for Systemic Lupus Erythematosus and Rheumatoid Arthritis","volume":"78","author":"Liu","year":"2019","journal-title":"Ann. Rheum. Dis."},{"key":"B29","doi-asserted-by":"publisher","first-page":"169","DOI":"10.3389\/fendo.2017.00169","article-title":"Autoimmune Thyroiditis and Myasthenia Gravis","volume":"8","author":"Lopomo","year":"2017","journal-title":"Front. Endocrinol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1016\/j.jaut.2016.06.001","article-title":"Dysregulation of Innate and Adaptive Serum Mediators Precedes Systemic Lupus Erythematosus Classification and Improves Prognostic Accuracy of Autoantibodies","volume":"74","author":"Lu","year":"2016","journal-title":"J. Autoimmun."},{"key":"B31","doi-asserted-by":"publisher","first-page":"121","DOI":"10.3109\/00207454.2010.539307","article-title":"Frequency of Autoimmune Diseases in Myasthenia Gravis: a Systematic Review","volume":"121","author":"Mao","year":"2011","journal-title":"Int. J. Neurosci."},{"key":"B32","doi-asserted-by":"publisher","first-page":"680","DOI":"10.1016\/j.survophthal.2016.04.006","article-title":"Autoimmune Disease: Conceptual History and Contributions of Ocular Immunology","volume":"61","author":"Margo","year":"2016","journal-title":"Surv. Ophthalmol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1210\/jcem.82.2.3749","article-title":"Mild Clinical Expression of Myasthenia Gravis Associated with Autoimmune Thyroid Diseases1","volume":"82","author":"Marin\u00f3","year":"1997","journal-title":"J. Clin. Endocrinol. Metab."},{"key":"B34","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/j.jaad.2005.08.047","article-title":"Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome (IPEX) Associated with Pemphigoid Nodularis: a Case Report and Review of the Literature","volume":"55","author":"McGinness","year":"2006","journal-title":"J. Am. Acad. Dermatol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1002\/art.20018","article-title":"Specific Autoantibodies Precede the Symptoms of Rheumatoid Arthritis: a Study of Serial Measurements in Blood Donors","volume":"50","author":"Nielen","year":"2004","journal-title":"Arthritis Rheum."},{"key":"B36","doi-asserted-by":"publisher","DOI":"10.1097\/RHU.0000000000001574","article-title":"Frequency of Polyautoimmunity in Patients with Rheumatoid Arthritis and Systemic Lupus Erythematosus","author":"Ordo\u00f1ez-Ca\u00f1izares","year":"2020","journal-title":"J. Clin. Rheumatol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"2363","DOI":"10.1101\/gr.1680803","article-title":"Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans","volume":"13","author":"Peri","year":"2003","journal-title":"Genome Res."},{"key":"B38","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.coi.2020.10.013","article-title":"The Innate Immune System and Cell Death in Autoinflammatory and Autoimmune Disease","volume":"67","author":"Place","year":"2020","journal-title":"Curr. Opin. Immunol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1016\/j.coi.2016.03.007","article-title":"Immunology by Numbers: Quantitation of Antigen Presentation Completes the Quantitative Milieu of Systems Immunology!","volume":"40","author":"Purcell","year":"2016","journal-title":"Curr. Opin. Immunol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2012\/593720","article-title":"Epigenetics and Autoimmune Diseases","volume":"2012","author":"Quintero-Ronderos","year":"2012","journal-title":"Autoimmune Dis."},{"key":"B41","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/gm305","article-title":"Emerging Patterns of Genetic Overlap across Autoimmune Disorders","volume":"4","author":"Richard-Miceli","year":"2012","journal-title":"Genome Med."},{"key":"B42","doi-asserted-by":"publisher","first-page":"322","DOI":"10.3389\/fimmu.2015.00322","article-title":"Antigen Presentation, Autoantigens, and Immune Regulation in Multiple Sclerosis and Other Autoimmune Diseases","volume":"6","author":"Riedhammer","year":"2015","journal-title":"Front. Immunol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1007\/bf03401948","article-title":"The Transporter Associated with Antigen Processing (TAP): Structural Integrity, Expression, Function, and its Clinical Relevance","volume":"7","author":"Ritz","year":"2001","journal-title":"Mol. Med."},{"key":"B44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2012\/254319","article-title":"Introducing Polyautoimmunity: Secondary Autoimmune Diseases No Longer Exist","volume":"2012","author":"Rojas-Villarraga","year":"2012","journal-title":"Autoimmune Dis."},{"key":"B45","doi-asserted-by":"publisher","first-page":"125sr121","DOI":"10.1126\/scitranslmed.3003504","article-title":"Treating Human Autoimmunity: Current Practice and Future Prospects","volume":"4","author":"Rosenblum","year":"2012","journal-title":"Sci. Transl. Med."},{"key":"B46","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/S0065-2776(07)96002-2","article-title":"Regulation of Interferon\u2010\u03b3 during Innate and Adaptive Immune Responses","volume":"96","author":"Schoenborn","year":"2007","journal-title":"Adv. Immunol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"D955","DOI":"10.1093\/nar\/gky1032","article-title":"Human Disease Ontology 2018 Update: Classification, Content and Workflow Expansion","volume":"47","author":"Schriml","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"B48","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a Software Environment for Integrated Models of Biomolecular Interaction Networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"B49","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1007\/400_2009_22","article-title":"Antigen Processing and Presentation in Multiple Sclerosis","volume":"51","author":"Stoeckle","year":"2009","journal-title":"Results Probl. Cel Differ."},{"key":"B50","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1016\/j.autrev.2007.11.007","article-title":"Stress as a Trigger of Autoimmune Disease","volume":"7","author":"Stojanovich","year":"2008","journal-title":"Autoimmun. Rev."},{"key":"B51","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abd7600","article-title":"Gene Expression Signatures of Target Tissues in Type 1 Diabetes, Lupus Erythematosus, Multiple Sclerosis, and Rheumatoid Arthritis","volume":"7","author":"Szymczak","year":"2021","journal-title":"Sci. Adv."},{"key":"B52","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1034\/j.1398-9995.1999.00099.x","article-title":"Biologic Functions of the IFN-Gamma Receptors","volume":"54","author":"Tau","year":"1999","journal-title":"Allergy"},{"key":"B53","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1038\/nature01621","article-title":"Association of the T-Cell Regulatory Gene CTLA4 with Susceptibility to Autoimmune Disease","volume":"423","author":"Ueda","year":"2003","journal-title":"Nature"},{"key":"B54","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1136\/annrheumdis-2019-215533","article-title":"Germline Genetic Patterns Underlying Familial Rheumatoid Arthritis, Systemic Lupus Erythematosus and Primary Sj\u00f6gren's Syndrome Highlight T Cell-Initiated Autoimmunity","volume":"79","author":"Wang","year":"2020","journal-title":"Ann. Rheum. Dis."},{"key":"B55","doi-asserted-by":"publisher","first-page":"e148674","DOI":"10.1172\/JCI148674","article-title":"Detection of Autoreactive CD4+ T Cells by MHC Class II Multimers in HLA-Linked Human Autoimmune Diseases","volume":"131","author":"Wieber","year":"2021","journal-title":"J. Clin. Invest."},{"key":"B56","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.gene.2016.04.024","article-title":"Exploring Information from the Topology beneath the Gene Ontology Terms to Improve Semantic Similarity Measures","volume":"586","author":"Zhang","year":"2016","journal-title":"Gene"},{"key":"B57","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.gene.2014.12.062","article-title":"Semantic Similarity Measurement between Gene Ontology Terms Based on Exclusively Inherited Shared Information","volume":"558","author":"Zhang","year":"2015","journal-title":"Gene"}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2021.758041\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,11,11]],"date-time":"2021-11-11T09:48:18Z","timestamp":1636624098000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2021.758041\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,11]]},"references-count":57,"alternative-id":["10.3389\/fgene.2021.758041"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2021.758041","relation":{},"ISSN":["1664-8021"],"issn-type":[{"type":"electronic","value":"1664-8021"}],"subject":[],"published":{"date-parts":[[2021,11,11]]},"article-number":"758041"}}