{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T04:45:31Z","timestamp":1774673131875,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,9,13]],"date-time":"2021-09-13T00:00:00Z","timestamp":1631491200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Basic Science Research Program","award":["NRF-2016R1D1A1B03933145"],"award-info":[{"award-number":["NRF-2016R1D1A1B03933145"]}]},{"name":"Bio-Synergy Research Project","award":["NRF-2013M3A9C4078158"],"award-info":[{"award-number":["NRF-2013M3A9C4078158"]}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Ministry of Education and the Ministry of Science"},{"name":"ICT and Future Planning"},{"name":"Korea Health Technology R&D Project through the Korea Health Industry Development Institute"},{"name":"Ministry of Health & Welfare, Republic of Korea","award":["HI16C2037010016"],"award-info":[{"award-number":["HI16C2037010016"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Drug repositioning reveals novel indications for existing drugs and in particular, diseases with no available drugs. Diverse computational drug repositioning methods have been proposed by measuring either drug-treated gene expression signatures or the proximity of drug targets and disease proteins found in prior networks. However, these methods do not explain which signaling subparts allow potential drugs to be selected, and do not consider polypharmacology, i.e. multiple targets of a known drug, in specific subparts.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, to address the limitations, we developed a subpathway-based polypharmacology drug repositioning method, PATHOME-Drug, based on drug-associated transcriptomes. Specifically, this tool locates subparts of signaling cascading related to phenotype changes (e.g. disease status changes), and identifies existing approved drugs such that their multiple targets are enriched in the subparts. We show that our method demonstrated better performance for detecting signaling context and specific drugs\/compounds, compared to WebGestalt and clusterProfiler, for both real biological and simulated datasets. We believe that our tool can successfully address the current shortage of targeted therapy agents.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The web-service is available at http:\/\/statgen.snu.ac.kr\/software\/pathome. The source codes and data are available at https:\/\/github.com\/labnams\/pathome-drug.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab566","type":"journal-article","created":{"date-parts":[[2021,9,10]],"date-time":"2021-09-10T03:13:58Z","timestamp":1631243638000},"page":"444-452","source":"Crossref","is-referenced-by-count":7,"title":["PATHOME-Drug: a subpathway-based polypharmacology drug-repositioning method"],"prefix":"10.1093","volume":"38","author":[{"given":"Seungyoon","family":"Nam","sequence":"first","affiliation":[{"name":"Department of Genome Medicine and Science, College of Medicine, Gachon University , 21565 Incheon, Korea"},{"name":"Department of Life Sciences, Gachon University , 13120 Seongnam, Korea"},{"name":"Gachon Institute of Genomic Medicine and Science, Gachon University Gil Medical Center , 21565 Incheon, Korea"},{"name":"Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University , 21999 Incheon, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3458-1440","authenticated-orcid":false,"given":"Sungyoung","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Genomic Medicine, Seoul National University Hospital , 03080 Seoul, Korea"},{"name":"Center for Precision Medicine, Seoul National University Hospital , 03080 Seoul, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sungjin","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Genome Medicine and Science, College of Medicine, Gachon University , 21565 Incheon, Korea"},{"name":"Gachon Institute of Genomic Medicine and Science, Gachon University Gil Medical Center , 21565 Incheon, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinhyuk","family":"Lee","sequence":"additional","affiliation":[{"name":"Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology , 34141 Daejeon, Korea"},{"name":"Department of Bioinformatics, University of Sciences and Technology , 34113 Daejeon, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0203-6069","authenticated-orcid":false,"given":"Aron","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology, Gachon University , 21999 Incheon, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yon Hui","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Biomedical Science, Hanyang University , 04763 Seoul, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8294-590X","authenticated-orcid":false,"given":"Taesung","family":"Park","sequence":"additional","affiliation":[{"name":"Interdisciplinary Program in Bioinformatics, Seoul National University , 08826 Seoul, Korea"},{"name":"Department of Statistics, Seoul National University , 08826 Seoul, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,13]]},"reference":[{"key":"2023020108414417800_btab566-B1","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nrg2918","article-title":"Network medicine: a network-based approach to human disease","volume":"12","author":"Barabasi","year":"2011","journal-title":"Nat. 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