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Meta\u2010analysis was performed by first processing data sets individually then cross\u2010study normalization and merging creating tissue\u2010specific gene expression matrices for subsequent analysis. Complementary single\u2010gene and network analyses using Significance Analysis of Microarrays (<jats:styled-content style=\"fixed-case\">SAM<\/jats:styled-content>) and Weighted Gene Co\u2010expression Network Analysis (<jats:styled-content style=\"fixed-case\">WGCNA<\/jats:styled-content>) were conducted to identify genes significantly associated with <jats:styled-content style=\"fixed-case\">DM<\/jats:styled-content>. Cell\u2010type enrichment was performed using <jats:styled-content style=\"fixed-case\">xC<\/jats:styled-content>ell.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>There were 544 differentially expressed genes (<jats:styled-content style=\"fixed-case\">FC<\/jats:styled-content> \u2265 1.3, <jats:italic>q<\/jats:italic> &lt; 0.05) in muscle and 300 in skin. There were 94 shared upregulated genes across tissues enriched in type I and <jats:styled-content style=\"fixed-case\">II<\/jats:styled-content> interferon (<jats:styled-content style=\"fixed-case\">IFN<\/jats:styled-content>) signaling and major histocompatibility complex (<jats:styled-content style=\"fixed-case\">MHC<\/jats:styled-content>) class I antigen\u2010processing pathways. In a network analysis, we identified eight significant gene modules in muscle and seven in skin. The most highly correlated modules were enriched in pathways consistent with the single\u2010gene analysis. Additional pathways uncovered by <jats:styled-content style=\"fixed-case\">WGCNA<\/jats:styled-content> included T\u2010cell activation and T\u2010cell receptor signaling. In the cell\u2010type enrichment analysis, both tissues were highly enriched in activated dendritic cells and M1 macrophages.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>There is striking similarity in gene expression across <jats:styled-content style=\"fixed-case\">DM<\/jats:styled-content> target tissues with enrichment of type I and <jats:styled-content style=\"fixed-case\">II IFN<\/jats:styled-content> pathways, <jats:styled-content style=\"fixed-case\">MHC<\/jats:styled-content> class I antigen\u2010processing, T\u2010cell activation, and antigen\u2010presenting cells. These results suggest <jats:styled-content style=\"fixed-case\">IFN<\/jats:styled-content>\u2010\u03b3 may contribute to the global <jats:styled-content style=\"fixed-case\">IFN<\/jats:styled-content> signature in <jats:styled-content style=\"fixed-case\">DM<\/jats:styled-content>, and altered auto\u2010antigen presentation through the class I <jats:styled-content style=\"fixed-case\">MHC<\/jats:styled-content> pathway may be important in disease pathogenesis.<\/jats:p><\/jats:sec>","DOI":"10.1002\/acr2.11081","type":"journal-article","created":{"date-parts":[[2019,11,9]],"date-time":"2019-11-09T16:33:15Z","timestamp":1573317195000},"page":"657-666","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Gene Expression Meta\u2010Analysis Reveals Concordance in Gene Activation, Pathway, and Cell\u2010Type Enrichment in Dermatomyositis Target Tissues"],"prefix":"10.1002","volume":"1","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0420-7933","authenticated-orcid":false,"given":"Jessica","family":"Neely","sequence":"first","affiliation":[{"name":"Department of Pediatrics University of California San Francisco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitry","family":"Rychkov","sequence":"additional","affiliation":[{"name":"Department of Pediatrics University of California San Francisco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manish","family":"Paranjpe","sequence":"additional","affiliation":[{"name":"Department of Pediatrics University of California San Francisco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Waterfield","sequence":"additional","affiliation":[{"name":"Department of Pediatrics University of California San Francisco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Pediatrics University of California San Francisco"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marina","family":"Sirota","sequence":"additional","affiliation":[{"name":"Department of Pediatrics University of California San Francisco"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,11,9]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/ana.20464"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.2119\/2006-00085.Baechler"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0029161"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/gene.2011.61"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1111\/bjd.15006"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1136\/annrheumdis-2012-202794"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1312625"},{"key":"e_1_2_7_9_1","doi-asserted-by":"publisher","DOI":"10.1002\/art.33368"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1002\/art.38628"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/art.40800"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2017.00074"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.3899\/jrheum.180455"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1193"},{"key":"e_1_2_7_15_1","unstructured":"The R Project for Statistical Computing. 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