{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,23]],"date-time":"2026-01-23T23:25:35Z","timestamp":1769210735386,"version":"3.49.0"},"reference-count":89,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T00:00:00Z","timestamp":1700524800000},"content-version":"vor","delay-in-days":60,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Harvard Medical School Aging Initiative Pilot"},{"name":"US National Institutes on Aging","award":["R01 AG082093"],"award-info":[{"award-number":["R01 AG082093"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35 CA232105"],"award-info":[{"award-number":["R35 CA232105"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 AG058816-01"],"award-info":[{"award-number":["R01 AG058816-01"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R01 CA258776"],"award-info":[{"award-number":["R01 CA258776"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cure Alzheimer's Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Charting microRNA (miRNA) regulation across pathways is key to characterizing their function. Yet, no method currently exists that can quantify how miRNAs regulate multiple interconnected pathways or prioritize them for their ability to regulate coordinate transcriptional programs. Existing methods primarily infer one-to-one relationships between miRNAs and pathways using differentially expressed genes. We introduce PanomiR, an in silico framework for studying the interplay of miRNAs and disease functions. PanomiR integrates gene expression, mRNA\u2013miRNA interactions and known biological pathways to reveal coordinated multi-pathway targeting by miRNAs. PanomiR utilizes pathway-activity profiling approaches, a pathway co-expression network and network clustering algorithms to prioritize miRNAs that target broad-scale transcriptional disease phenotypes. It directly resolves differential regulation of pathways, irrespective of their differential gene expression, and captures co-activity to establish functional pathway groupings and the miRNAs that may regulate them. PanomiR uses a systems biology approach to provide broad but precise insights into miRNA-regulated functional programs. It is available at https:\/\/bioconductor.org\/packages\/PanomiR.<\/jats:p>","DOI":"10.1093\/bib\/bbad418","type":"journal-article","created":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T02:24:52Z","timestamp":1700533492000},"source":"Crossref","is-referenced-by-count":6,"title":["PanomiR: a systems biology framework for analysis of multi-pathway targeting by miRNAs"],"prefix":"10.1093","volume":"24","author":[{"given":"Pourya","family":"Naderi Yeganeh","sequence":"first","affiliation":[{"name":"Harvard Medical School , Boston, MA , USA"},{"name":"Department of Pathology, Beth Israel Deaconess Medical Center , Boston, MA , USA"},{"name":"Harvard Medical School Initiative for RNA Medicine , Boston, MA , USA"}]},{"given":"Yue Y","family":"Teo","sequence":"additional","affiliation":[{"name":"National University of Singapore , Singapore"},{"name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL) , Lausanne , Switzerland"}]},{"given":"Dimitra","family":"Karagkouni","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA , USA"},{"name":"Department of Pathology, Beth Israel Deaconess Medical Center , Boston, MA , USA"},{"name":"Harvard Medical School Initiative for RNA Medicine , Boston, MA , USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA , USA"}]},{"given":"Yered","family":"Pita-Ju\u00e1rez","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA , USA"},{"name":"Department of Pathology, Beth Israel Deaconess Medical Center , Boston, MA , USA"},{"name":"Harvard Medical School Initiative for RNA Medicine , Boston, MA , USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA , USA"}]},{"given":"Sarah L","family":"Morgan","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA , USA"},{"name":"Centre for Neuroscience , Surgery and Trauma, Blizard Institute, , London E1 2AT , UK"},{"name":"Queen Mary University of London , Surgery and Trauma, Blizard Institute, , London E1 2AT , UK"}]},{"given":"Frank J","family":"Slack","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA , USA"},{"name":"Department of Pathology, Beth Israel Deaconess Medical Center , Boston, MA , USA"},{"name":"Harvard Medical School Initiative for RNA Medicine , Boston, MA , USA"}]},{"given":"Ioannis S","family":"Vlachos","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA , USA"},{"name":"Department of Pathology, Beth Israel Deaconess Medical Center , Boston, MA , USA"},{"name":"Harvard Medical School Initiative for RNA Medicine , Boston, MA , USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA , USA"}]},{"given":"Winston A","family":"Hide","sequence":"additional","affiliation":[{"name":"Harvard Medical School , Boston, MA , USA"},{"name":"Department of Pathology, Beth Israel Deaconess Medical Center , Boston, MA , USA"},{"name":"Harvard Medical School Initiative for RNA Medicine , Boston, MA , USA"}]}],"member":"286","published-online":{"date-parts":[[2023,11,20]]},"reference":[{"key":"2023112102242385000_ref1","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1101\/gr.082701.108","article-title":"Most mammalian mRNAs are conserved targets of microRNAs","volume":"19","author":"Friedman","year":"2009","journal-title":"Genome Res"},{"key":"2023112102242385000_ref2","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1016\/j.cell.2019.10.017","article-title":"The role of non-coding RNAs in oncology","volume":"179","author":"Slack","year":"2019","journal-title":"Cell"},{"key":"2023112102242385000_ref3","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/S1672-0229(08)60044-3","article-title":"A brief review on the mechanisms of miRNA regulation","volume":"7","author":"Cai","year":"2009","journal-title":"Genomics Proteomics 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