{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T01:53:16Z","timestamp":1774489996171,"version":"3.50.1"},"reference-count":84,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T00:00:00Z","timestamp":1576108800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Russian-Armenian University Internal Grant","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["idSEM program: FKZ 031L0026"],"award-info":[{"award-number":["idSEM program: FKZ 031L0026"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["WTZ ARM II-010"],"award-info":[{"award-number":["WTZ ARM II-010"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"State Committee of Science MES RA","award":["16GE-025"],"award-info":[{"award-number":["16GE-025"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pharmaceutics"],"abstract":"<jats:p>Drug repositioning can save considerable time and resources and significantly speed up the drug development process. The increasing availability of drug action and disease-associated transcriptome data makes it an attractive source for repositioning studies. Here, we have developed a transcriptome-guided approach for drug\/biologics repositioning based on multi-layer self-organizing maps (ml-SOM). It allows for analyzing multiple transcriptome datasets by segmenting them into layers of drug action- and disease-associated transcriptome data. A comparison of expression changes in clusters of functionally related genes across the layers identifies \u201cdrug target\u201d spots in disease layers and evaluates the repositioning possibility of a drug. The repositioning potential for two approved biologics drugs (infliximab and brodalumab) confirmed the drugs\u2019 action for approved diseases (ulcerative colitis and Crohn\u2019s disease for infliximab and psoriasis for brodalumab). We showed the potential efficacy of infliximab for the treatment of sarcoidosis, but not chronic obstructive pulmonary disease (COPD). Brodalumab failed to affect dysregulated functional gene clusters in Crohn\u2019s disease (CD) and systemic juvenile idiopathic arthritis (SJIA), clearly indicating that it may not be effective in the treatment of these diseases. In conclusion, ml-SOM offers a novel approach for transcriptome-guided drug repositioning that could be particularly useful for biologics drugs.<\/jats:p>","DOI":"10.3390\/pharmaceutics11120677","type":"journal-article","created":{"date-parts":[[2019,12,12]],"date-time":"2019-12-12T11:06:41Z","timestamp":1576148801000},"page":"677","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Transcriptome-Guided Drug Repositioning"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6851-1056","authenticated-orcid":false,"given":"Arsen","family":"Arakelyan","sequence":"first","affiliation":[{"name":"Institute of Biomedicine and Pharmacy, Russian-Armenian University, 0051 Yerevan, Armenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8525-420X","authenticated-orcid":false,"given":"Lilit","family":"Nersisyan","sequence":"additional","affiliation":[{"name":"Group of Bioinformatics, Institute of Molecular Biology NAS RA, 0014 Yerevan, Armenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Nikoghosyan","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine and Pharmacy, Russian-Armenian University, 0051 Yerevan, Armenia"},{"name":"Group of Bioinformatics, Institute of Molecular Biology NAS RA, 0014 Yerevan, Armenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Siras","family":"Hakobyan","sequence":"additional","affiliation":[{"name":"Group of Bioinformatics, Institute of Molecular Biology NAS RA, 0014 Yerevan, Armenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1032-1073","authenticated-orcid":false,"given":"Arman","family":"Simonyan","sequence":"additional","affiliation":[{"name":"Institute of Biomedicine and Pharmacy, Russian-Armenian University, 0051 Yerevan, Armenia"},{"name":"Group of Bioinformatics, Institute of Molecular Biology NAS RA, 0014 Yerevan, Armenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lydia","family":"Hopp","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henry","family":"Loeffler-Wirth","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2242-4678","authenticated-orcid":false,"given":"Hans","family":"Binder","sequence":"additional","affiliation":[{"name":"Interdisciplinary Centre for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2019,12,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1038\/nrd1468","article-title":"Drug repositioning: Identifying and developing new uses for existing drugs","volume":"3","author":"Ashburn","year":"2004","journal-title":"Nat. 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