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Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https:\/\/www.ccb.uni-saarland.de\/mirtargetlink2.<\/jats:p>","DOI":"10.1093\/nar\/gkab297","type":"journal-article","created":{"date-parts":[[2021,4,12]],"date-time":"2021-04-12T12:05:12Z","timestamp":1618229112000},"page":"W409-W416","source":"Crossref","is-referenced-by-count":182,"title":["miRTargetLink 2.0\u2014interactive miRNA target gene and target pathway networks"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8223-3750","authenticated-orcid":false,"given":"Fabian","family":"Kern","sequence":"first","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernesto","family":"Aparicio-Puerta","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongping","family":"Li","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1967-2918","authenticated-orcid":false,"given":"Tobias","family":"Fehlmann","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9523-7566","authenticated-orcid":false,"given":"Tim","family":"Kehl","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viktoria","family":"Wagner","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kamalika","family":"Ray","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Ludwig","sequence":"additional","affiliation":[{"name":"Center for Human and Molecular Biology, Institute of Human Genetics, Saarland University, 66421 Homburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans-Peter","family":"Lenhof","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbr\u00fccken, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eckart","family":"Meese","sequence":"additional","affiliation":[{"name":"Center for Human and Molecular Biology, Institute of Human Genetics, Saarland University, 66421 Homburg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5361-0895","authenticated-orcid":false,"given":"Andreas","family":"Keller","sequence":"additional","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbr\u00fccken, Germany"},{"name":"Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford 94304, CA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,5,1]]},"reference":[{"key":"2021070812035872100_B1","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/s43587-021-00042-6","article-title":"Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson\u2019s disease progression","volume":"1","author":"Kern","year":"2021","journal-title":"Nat. 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