{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,28]],"date-time":"2026-01-28T20:06:25Z","timestamp":1769630785850,"version":"3.49.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2022,6,1]],"date-time":"2022-06-01T00:00:00Z","timestamp":1654041600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["P34783"],"award-info":[{"award-number":["P34783"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004061","name":"National Bank of Austria","doi-asserted-by":"publisher","award":["18279"],"award-info":[{"award-number":["18279"]}],"id":[{"id":"10.13039\/501100004061","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003508","name":"University of Valencia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003508","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,11]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>MicroRNAs have been shown to be able to modulate the tumor microenvironment and the immune response and hence could be interesting biomarkers and therapeutic targets in immuno-oncology; however, dedicated analysis tools are missing. Here, we present a user-friendly web platform MIO and a Python toolkit miopy integrating various methods for visualization and analysis of provided or custom bulk microRNA and gene expression data. We include regularized regression and survival analysis and provide information of 40 microRNA target prediction tools as well as a collection of curated immune related gene and microRNA signatures and processed TCGA data including estimations of infiltrated immune cells and the immunophenoscore. The integration of several machine learning methods enables the selection of prognostic and predictive microRNAs and gene interaction network biomarkers.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/mio.icbi.at, https:\/\/github.com\/icbi-lab\/mio and https:\/\/github.com\/icbi-lab\/miopy.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac366","type":"journal-article","created":{"date-parts":[[2022,6,1]],"date-time":"2022-06-01T12:14:12Z","timestamp":1654085652000},"page":"3665-3667","source":"Crossref","is-referenced-by-count":2,"title":["MIO: microRNA target analysis system for immuno-oncology"],"prefix":"10.1093","volume":"38","author":[{"given":"Pablo","family":"Monfort-Lanzas","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria"},{"name":"Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria"}]},{"given":"Raphael","family":"Gronauer","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria"}]},{"given":"Leonie","family":"Madersbacher","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria"}]},{"given":"Christoph","family":"Schatz","sequence":"additional","affiliation":[{"name":"Institute of Pathology, Neuropathology and Molecular Pathology, Medical University of Innsbruck , 6020 Innsbruck, Austria"}]},{"given":"Dietmar","family":"Rieder","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4055-3841","authenticated-orcid":false,"given":"Hubert","family":"Hackl","sequence":"additional","affiliation":[{"name":"Institute of Bioinformatics, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria"}]}],"member":"286","published-online":{"date-parts":[[2022,6,1]]},"reference":[{"key":"2023041405361315500_","doi-asserted-by":"crossref","first-page":"5635","DOI":"10.1158\/0008-5472.CAN-11-0489","article-title":"microRNA-associated progression pathways and potential therapeutic targets identified by integrated mRNA and microRNA expression profiling in breast cancer","volume":"71","author":"Buffa","year":"2011","journal-title":"Cancer Res"},{"key":"2023041405361315500_","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.celrep.2016.12.019","article-title":"Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade","volume":"18","author":"Charoentong","year":"2017","journal-title":"Cell Rep"},{"key":"2023041405361315500_","doi-asserted-by":"crossref","first-page":"5228","DOI":"10.1038\/s41467-018-07657-1","article-title":"Pan-cancer characterisation of microRNA across cancer hallmarks reveals microRNA-mediated downregulation of tumour suppressors","volume":"9","author":"Dhawan","year":"2018","journal-title":"Nat. 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