{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T18:44:52Z","timestamp":1791398692373,"version":"4.3.3"},"reference-count":78,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2018,9,10]],"date-time":"2018-09-10T00:00:00Z","timestamp":1536537600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"NIH-Oxford-Cambridge Scholars Program"},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["Clinical PhD Programme"],"award-info":[{"award-number":["Clinical PhD Programme"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["Clinical PhD Programme"],"award-info":[{"award-number":["Clinical PhD Programme"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","award":["Intramural Program"],"award-info":[{"award-number":["Intramural Program"]}],"id":[{"id":"10.13039\/100000069","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1007458","type":"journal-article","created":{"date-parts":[[2018,9,10]],"date-time":"2018-09-10T17:23:19Z","timestamp":1536600199000},"page":"e1007458","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":45,"title":["Reduced monocyte and macrophage TNFSF15\/TL1A expression is associated with susceptibility to inflammatory bowel disease"],"prefix":"10.1371","volume":"14","author":[{"given":"Arianne C.","family":"Richard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James E.","family":"Peters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Savinykh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5711-9385","authenticated-orcid":true,"given":"James C.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2357-2154","authenticated-orcid":true,"given":"Eric T.","family":"Hawley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9279-7875","authenticated-orcid":true,"given":"Fran\u00e7oise","family":"Meylan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard M.","family":"Siegel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul A.","family":"Lyons","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kenneth G. C.","family":"Smith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,9,10]]},"reference":[{"issue":"3","key":"ref1","doi-asserted-by":"crossref","first-page":"411","DOI":"10.4161\/gmic.29330","article-title":"The interplay between the gut microbiota and the immune system","volume":"5","author":"MB Geuking","year":"2014","journal-title":"Gut Microbes"},{"issue":"4","key":"ref2","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1097\/BOR.0000000000000190","article-title":"The functional impact of the intestinal microbiome on mucosal immunity and systemic autoimmunity","volume":"27","author":"RS Longman","year":"2015","journal-title":"Curr Opin Rheumatol"},{"issue":"11","key":"ref3","doi-asserted-by":"crossref","first-page":"1653","DOI":"10.1136\/gutjnl-2012-303955","article-title":"Recent advances in inflammatory bowel disease: mucosal immune cells in intestinal inflammation","volume":"62","author":"MZ Cader","year":"2013","journal-title":"Gut"},{"issue":"9","key":"ref4","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1038\/ng.3359","article-title":"Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations","volume":"47","author":"JZ Liu","year":"2015","journal-title":"Nat Genet"},{"issue":"7422","key":"ref5","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nature11582","article-title":"Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease","volume":"491","author":"L Jostins","year":"2012","journal-title":"Nature"},{"issue":"7662","key":"ref6","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nature22969","article-title":"Fine-mapping inflammatory bowel disease loci to single-variant resolution","volume":"547","author":"H Huang","year":"2017","journal-title":"Nature"},{"issue":"6837","key":"ref7","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/35079114","article-title":"A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease","volume":"411","author":"Y Ogura","year":"2001","journal-title":"Nature"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nm.2069","article-title":"NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation","volume":"16","author":"R Cooney","year":"2010","journal-title":"Nat Med"},{"issue":"6","key":"ref9","doi-asserted-by":"crossref","first-page":"3455","DOI":"10.1073\/pnas.0530276100","article-title":"Gene-environment interaction modulated by allelic heterogeneity in inflammatory diseases","volume":"100","author":"M Chamaillard","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"11","key":"ref10","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1136\/gut.2003.032805","article-title":"NOD2 (CARD15) mutations in Crohn's disease are associated with diminished mucosal alpha-defensin expression","volume":"53","author":"J Wehkamp","year":"2004","journal-title":"Gut"},{"issue":"7219","key":"ref11","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nature07416","article-title":"A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells","volume":"456","author":"K Cadwell","year":"2008","journal-title":"Nature"},{"issue":"21","key":"ref12","doi-asserted-by":"crossref","first-page":"7741","DOI":"10.1073\/pnas.1407001111","article-title":"Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense","volume":"111","author":"KG Lassen","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7489","key":"ref13","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1038\/nature13044","article-title":"A Crohn's disease variant in Atg16l1 enhances its degradation by caspase 3","volume":"506","author":"A Murthy","year":"2014","journal-title":"Nature"},{"issue":"16","key":"ref14","doi-asserted-by":"crossref","first-page":"8673","DOI":"10.1074\/jbc.M116.715870","article-title":"IL23R (Interleukin 23 Receptor) Variants Protective against Inflammatory Bowel Diseases (IBD) Display Loss of Function due to Impaired Protein Stability and Intracellular Trafficking","volume":"291","author":"D Sivanesan","year":"2016","journal-title":"J Biol Chem"},{"issue":"2","key":"ref15","doi-asserted-by":"crossref","first-page":"e17160","DOI":"10.1371\/journal.pone.0017160","article-title":"The IL23R R381Q gene variant protects against immune-mediated diseases by impairing IL-23-induced Th17 effector response in humans","volume":"6","author":"P Di Meglio","year":"2011","journal-title":"PLoS One"},{"issue":"10","key":"ref16","doi-asserted-by":"crossref","first-page":"e25038","DOI":"10.1371\/journal.pone.0025038","article-title":"Functional studies on the IBD susceptibility gene IL23R implicate reduced receptor function in the protective genetic variant R381Q","volume":"6","author":"S Pidasheva","year":"2011","journal-title":"PLoS One"},{"issue":"23","key":"ref17","doi-asserted-by":"crossref","first-page":"9560","DOI":"10.1073\/pnas.1017854108","article-title":"Inflammatory disease protective R381Q IL23 receptor polymorphism results in decreased primary CD4+ and CD8+ human T-cell functional responses","volume":"108","author":"R Sarin","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"ref18","doi-asserted-by":"crossref","first-page":"e1005908","DOI":"10.1371\/journal.pgen.1005908","article-title":"Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease","volume":"12","author":"JE Peters","year":"2016","journal-title":"PLoS Genet"},{"issue":"1","key":"ref19","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1186\/s13073-016-0329-5","article-title":"Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network","volume":"8","author":"AC Richard","year":"2016","journal-title":"Genome Med"},{"issue":"5","key":"ref20","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1038\/ng.2205","article-title":"Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles","volume":"44","author":"BP Fairfax","year":"2012","journal-title":"Nat Genet"},{"issue":"3","key":"ref21","doi-asserted-by":"crossref","first-page":"e1006641","DOI":"10.1371\/journal.pgen.1006641","article-title":"Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease","volume":"13","author":"JK Baillie","year":"2017","journal-title":"PLoS Genet"},{"issue":"3","key":"ref22","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1053\/j.gastro.2011.05.048","article-title":"HLA-Cw*1202-B*5201-DRB1*1502 haplotype increases risk for ulcerative colitis but reduces risk for Crohn's disease","volume":"141","author":"Y Okada","year":"2011","journal-title":"Gastroenterology"},{"issue":"4","key":"ref23","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1053\/j.gastro.2012.12.021","article-title":"A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population","volume":"144","author":"K Yamazaki","year":"2013","journal-title":"Gastroenterology"},{"issue":"3","key":"ref24","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1189\/jlb.3RI0315-095R","article-title":"The TNF-family cytokine TL1A: from lymphocyte costimulator to disease co-conspirator","volume":"98","author":"AC Richard","year":"2015","journal-title":"J Leukoc Biol"},{"issue":"8","key":"ref25","doi-asserted-by":"crossref","first-page":"3567","DOI":"10.4049\/jimmunol.1401220","article-title":"The TNF-family ligand TL1A and its receptor DR3 promote T cell-mediated allergic immunopathology by enhancing differentiation and pathogenicity of IL-9-producing T cells","volume":"194","author":"AC Richard","year":"2015","journal-title":"J Immunol"},{"issue":"3","key":"ref26","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/S1074-7613(02)00283-2","article-title":"TL1A is a TNF-like ligand for DR3 and TR6\/DcR3 and functions as a T cell costimulator","volume":"16","author":"TS Migone","year":"2002","journal-title":"Immunity"},{"issue":"4","key":"ref27","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1038\/mi.2013.114","article-title":"The TNF-family cytokine TL1A promotes allergic immunopathology through group 2 innate lymphoid cells","volume":"7","author":"F Meylan","year":"2014","journal-title":"Mucosal Immunol"},{"issue":"3","key":"ref28","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/mi.2013.92","article-title":"TNF superfamily member TL1A elicits type 2 innate lymphoid cells at mucosal barriers","volume":"7","author":"X Yu","year":"2014","journal-title":"Mucosal Immunol"},{"issue":"1","key":"ref29","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.immuni.2008.04.021","article-title":"The TNF-family receptor DR3 is essential for diverse T cell-mediated inflammatory diseases","volume":"29","author":"F Meylan","year":"2008","journal-title":"Immunity"},{"issue":"9","key":"ref30","doi-asserted-by":"crossref","first-page":"2606","DOI":"10.1002\/eji.201141477","article-title":"Triggering of TNFRSF25 promotes CD8(+) T-cell responses and anti-tumor immunity","volume":"41","author":"TJ Slebioda","year":"2011","journal-title":"Eur J Immunol"},{"issue":"8","key":"ref31","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1084\/jem.20140678","article-title":"CX(3)CR1(+) mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22","volume":"211","author":"RS Longman","year":"2014","journal-title":"J Exp Med"},{"issue":"2","key":"ref32","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1016\/j.clim.2010.07.001","article-title":"High intestinal and systemic levels of decoy receptor 3 (DcR3) and its ligand TL1A in active ulcerative colitis","volume":"137","author":"G Bamias","year":"2010","journal-title":"Clin Immunol"},{"issue":"9","key":"ref33","doi-asserted-by":"crossref","first-page":"4868","DOI":"10.4049\/jimmunol.171.9.4868","article-title":"Expression, localization, and functional activity of TL1A, a novel Th1-polarizing cytokine in inflammatory bowel disease","volume":"171","author":"G Bamias","year":"2003","journal-title":"J Immunol"},{"issue":"1","key":"ref34","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.dld.2011.09.002","article-title":"Differential expression of the TL1A\/DcR3 system of TNF\/TNFR-like proteins in large vs. small intestinal Crohn's disease","volume":"44","author":"G Bamias","year":"2012","journal-title":"Dig Liver Dis"},{"issue":"1","key":"ref35","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1016\/j.clim.2004.02.007","article-title":"Potential role for TL1A, the new TNF-family member and potent costimulator of IFN-gamma, in mucosal inflammation","volume":"112","author":"JL Prehn","year":"2004","journal-title":"Clin Immunol"},{"issue":"5","key":"ref36","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1038\/mi.2012.124","article-title":"TL1A\/TNFSF15 directly induces proinflammatory cytokines, including TNFalpha, from CD3+CD161+ T cells to exacerbate gut inflammation","volume":"6","author":"S Jin","year":"2013","journal-title":"Mucosal Immunol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"425915","DOI":"10.1155\/2013\/425915","article-title":"High intestinal and systemic levels of interleukin-23\/T-helper 17 pathway in Chinese patients with inflammatory bowel disease","volume":"2013","author":"L Song","year":"2013","journal-title":"Mediators Inflamm"},{"issue":"6","key":"ref38","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1093\/hmg\/ddp005","article-title":"TNFSF15 transcripts from risk haplotype for Crohn's disease are overexpressed in stimulated T cells","volume":"18","author":"Y Kakuta","year":"2009","journal-title":"Hum Mol Genet"},{"issue":"3","key":"ref39","doi-asserted-by":"crossref","first-page":"e4719","DOI":"10.1371\/journal.pone.0004719","article-title":"IBD-associated TL1A gene (TNFSF15) haplotypes determine increased expression of TL1A protein","volume":"4","author":"KS Michelsen","year":"2009","journal-title":"PLoS One"},{"issue":"12","key":"ref40","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.1136\/gut.2011.241877","article-title":"Association of TNFSF15 polymorphism with irritable bowel syndrome","volume":"60","author":"M Zucchelli","year":"2011","journal-title":"Gut"},{"issue":"37","key":"ref41","doi-asserted-by":"crossref","first-page":"13451","DOI":"10.1073\/pnas.1404178111","article-title":"A TNFSF15 disease-risk polymorphism increases pattern-recognition receptor-induced signaling through caspase-8-induced IL-1","volume":"111","author":"M Hedl","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6175","key":"ref42","doi-asserted-by":"crossref","first-page":"1246980","DOI":"10.1126\/science.1246980","article-title":"Common genetic variants modulate pathogen-sensing responses in human dendritic cells","volume":"343","author":"MN Lee","year":"2014","journal-title":"Science"},{"issue":"6183","key":"ref43","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1126\/science.1249547","article-title":"Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes","volume":"344","author":"T Raj","year":"2014","journal-title":"Science"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"31429","DOI":"10.1038\/srep31429","article-title":"Fine-mapping analysis revealed complex pleiotropic effect and tissue-specific regulatory mechanism of TNFSF15 in primary biliary cholangitis, Crohn's disease and leprosy","volume":"6","author":"Y Sun","year":"2016","journal-title":"Sci Rep"},{"issue":"6235","key":"ref45","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","year":"2015","journal-title":"Science"},{"issue":"3","key":"ref46","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/j.cell.2016.09.025","article-title":"Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens","volume":"167","author":"Y Nedelec","year":"2016","journal-title":"Cell"},{"issue":"7675","key":"ref47","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature24277","article-title":"Genetic effects on gene expression across human tissues","volume":"550","author":"GTEx Consortium","year":"2017","journal-title":"Nature"},{"issue":"5","key":"ref48","doi-asserted-by":"crossref","first-page":"e1004383","DOI":"10.1371\/journal.pgen.1004383","article-title":"Bayesian test for colocalisation between pairs of genetic association studies using summary statistics","volume":"10","author":"C Giambartolomei","year":"2014","journal-title":"PLoS Genet"},{"issue":"10","key":"ref49","doi-asserted-by":"crossref","first-page":"1238","DOI":"10.1038\/ng.2756","article-title":"Systematic identification of trans eQTLs as putative drivers of known disease associations","volume":"45","author":"HJ Westra","year":"2013","journal-title":"Nat Genet"},{"issue":"6175","key":"ref50","doi-asserted-by":"crossref","first-page":"1246949","DOI":"10.1126\/science.1246949","article-title":"Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression","volume":"343","author":"BP Fairfax","year":"2014","journal-title":"Science"},{"issue":"5","key":"ref51","doi-asserted-by":"crossref","first-page":"e10693","DOI":"10.1371\/journal.pone.0010693","article-title":"Genetics and beyond\u2014the transcriptome of human monocytes and disease susceptibility","volume":"5","author":"T Zeller","year":"2010","journal-title":"PLoS One"},{"issue":"7","key":"ref52","doi-asserted-by":"crossref","first-page":"4033","DOI":"10.4049\/jimmunol.178.7.4033","article-title":"The T cell costimulator TL1A is induced by FcgammaR signaling in human monocytes and dendritic cells","volume":"178","author":"JL Prehn","year":"2007","journal-title":"J Immunol"},{"issue":"11","key":"ref53","doi-asserted-by":"crossref","first-page":"3239","DOI":"10.1002\/eji.200839087","article-title":"Microbial induction of inflammatory bowel disease associated gene TL1A (TNFSF15) in antigen presenting cells","volume":"39","author":"DQ Shih","year":"2009","journal-title":"Eur J Immunol"},{"issue":"5","key":"ref54","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1084\/jem.20072528","article-title":"Essential role of TNF receptor superfamily 25 (TNFRSF25) in the development of allergic lung inflammation","volume":"205","author":"L Fang","year":"2008","journal-title":"J Exp Med"},{"issue":"10","key":"ref55","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1038\/ni.2967","article-title":"Constant replenishment from circulating monocytes maintains the macrophage pool in the intestine of adult mice","volume":"15","author":"CC Bain","year":"2014","journal-title":"Nat Immunol"},{"issue":"3","key":"ref56","doi-asserted-by":"crossref","first-page":"502","DOI":"10.1016\/j.immuni.2009.06.025","article-title":"Intestinal lamina propria dendritic cell subsets have different origin and functions","volume":"31","author":"C Varol","year":"2009","journal-title":"Immunity"},{"issue":"3","key":"ref57","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1016\/j.immuni.2009.08.010","article-title":"Origin of the lamina propria dendritic cell network","volume":"31","author":"M Bogunovic","year":"2009","journal-title":"Immunity"},{"issue":"1","key":"ref58","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1111\/imr.12192","article-title":"Macrophages in intestinal homeostasis and inflammation","volume":"260","author":"CC Bain","year":"2014","journal-title":"Immunol Rev"},{"issue":"11","key":"ref59","doi-asserted-by":"crossref","first-page":"2457","DOI":"10.1084\/jem.20072378","article-title":"The Death Receptor 3-TNF-like protein 1A pathway drives adverse bone pathology in inflammatory arthritis","volume":"205","author":"MJ Bull","year":"2008","journal-title":"J Exp Med"},{"issue":"2","key":"ref60","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1038\/mi.2010.67","article-title":"The TNF-family cytokine TL1A drives IL-13-dependent small intestinal inflammation","volume":"4","author":"F Meylan","year":"2011","journal-title":"Mucosal Immunol"},{"issue":"5","key":"ref61","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1084\/jem.20071364","article-title":"TL1A-DR3 interaction regulates Th17 cell function and Th17-mediated autoimmune disease","volume":"205","author":"BP Pappu","year":"2008","journal-title":"J Exp Med"},{"issue":"2","key":"ref62","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1053\/j.gastro.2008.04.037","article-title":"TL1A (TNFSF15) regulates the development of chronic colitis by modulating both T-helper 1 and T-helper 17 activation","volume":"135","author":"H Takedatsu","year":"2008","journal-title":"Gastroenterology"},{"issue":"11","key":"ref63","doi-asserted-by":"crossref","first-page":"5420","DOI":"10.4049\/jimmunol.1301475","article-title":"TNF-like ligand 1A (TL1A) gene knockout leads to ameliorated collagen-induced arthritis in mice: implication of TL1A in humoral immune responses","volume":"191","author":"X Wang","year":"2013","journal-title":"J Immunol"},{"issue":"11","key":"ref64","doi-asserted-by":"crossref","first-page":"7002","DOI":"10.4049\/jimmunol.172.11.7002","article-title":"TL1A synergizes with IL-12 and IL-18 to enhance IFN-gamma production in human T cells and NK cells","volume":"172","author":"KA Papadakis","year":"2004","journal-title":"J Immunol"},{"issue":"1","key":"ref65","doi-asserted-by":"crossref","first-page":"377","DOI":"10.4049\/jimmunol.1502466","article-title":"A Novel Role for TL1A\/DR3 in Protection against Intestinal Injury and Infection","volume":"197","author":"LG Jia","year":"2016","journal-title":"J Immunol"},{"issue":"8","key":"ref66","doi-asserted-by":"crossref","first-page":"2335","DOI":"10.1002\/eji.201445213","article-title":"Human group3 innate lymphoid cells express DR3 and respond to TL1A with enhanced IL-22 production and IL-2-dependent proliferation","volume":"45","author":"YO Ahn","year":"2015","journal-title":"Eur J Immunol"},{"issue":"3","key":"ref67","doi-asserted-by":"crossref","first-page":"282","DOI":"10.1038\/nm1720","article-title":"Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens","volume":"14","author":"Y Zheng","year":"2008","journal-title":"Nat Med"},{"issue":"1","key":"ref68","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/mi.2011.54","article-title":"Opposing consequences of IL-23 signaling mediated by innate and adaptive cells in chemically induced colitis in mice","volume":"5","author":"JH Cox","year":"2012","journal-title":"Mucosal Immunol"},{"issue":"6","key":"ref69","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.immuni.2008.11.003","article-title":"Innate and adaptive interleukin-22 protects mice from inflammatory bowel disease","volume":"29","author":"LA Zenewicz","year":"2008","journal-title":"Immunity"},{"issue":"6","key":"ref70","doi-asserted-by":"crossref","first-page":"898","DOI":"10.1016\/j.immuni.2014.12.010","article-title":"NOD1 and NOD2: signaling, host defense, and inflammatory disease","volume":"41","author":"R Caruso","year":"2014","journal-title":"Immunity"},{"issue":"19","key":"ref71","doi-asserted-by":"crossref","first-page":"2363","DOI":"10.1093\/bioinformatics\/btq431","article-title":"A framework for oligonucleotide microarray preprocessing","volume":"26","author":"BS Carvalho","year":"2010","journal-title":"Bioinformatics"},{"issue":"5","key":"ref72","doi-asserted-by":"crossref","first-page":"e1000770","DOI":"10.1371\/journal.pcbi.1000770","article-title":"A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies","volume":"6","author":"O Stegle","year":"2010","journal-title":"PLoS Comput Biol"},{"issue":"11","key":"ref73","doi-asserted-by":"crossref","first-page":"1447","DOI":"10.1093\/bioinformatics\/btp169","article-title":"Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x","volume":"25","author":"VJ Carey","year":"2009","journal-title":"Bioinformatics"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1007\/978-1-4939-3578-9_16","article-title":"Visualizing Genomic Data Using Gviz and Bioconductor","volume":"1418","author":"F Hahne","year":"2016","journal-title":"Methods Mol Biol"},{"key":"ref75","unstructured":"Siegel RM, Meylan F, Song Y-J, inventors; The United States of America, as represented by the Secretary, Dept. of Health and Human Services (Washington, DC, US), assignee. Antibodies that bind to TL1A and methods of treating inflammatory or autoimmune disease comprising administering such antibodies. United States patent US 9068003 B2. 2015."},{"issue":"D1","key":"ref76","doi-asserted-by":"crossref","first-page":"D762","DOI":"10.1093\/nar\/gkx1020","article-title":"The UCSC Genome Browser database: 2018 update","volume":"46","author":"J Casper","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"D56","DOI":"10.1093\/nar\/gks1172","article-title":"ENCODE data in the UCSC Genome Browser: year 5 update","volume":"41","author":"KR Rosenbloom","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"6225","key":"ref78","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1126\/science.1259418","article-title":"Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells","volume":"347","author":"E Arner","year":"2015","journal-title":"Science"}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1007458","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,9]],"date-time":"2020-11-09T10:39:13Z","timestamp":1604918353000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1007458"}},"subtitle":[],"editor":[{"given":"Vincent","family":"Plagnol","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,9,10]]},"references-count":78,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2018,9,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1007458","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,9,10]]}}}