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There is an urgent need to develop innovative methodologies and tools that can characterize and visualize functional consequences of cancer risk gene and miRNA pairs while analyzing the tumor and normal samples simultaneously.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>We developed an innovative bioinformatics tool for visualizing functional annotation of miRNA-mRNA pairs in a network, known as <jats:italic>MMiRNA-Viewer<\/jats:italic><jats:sup><jats:italic>2<\/jats:italic><\/jats:sup>. The tool takes mRNA and miRNA interaction pairs and visualizes mRNA and miRNA regulation network. Moreover, our <jats:italic>MMiRNA-Viewer<\/jats:italic><jats:sup><jats:italic>2<\/jats:italic><\/jats:sup> web server integrates and displays the mRNA and miRNA gene annotation information, signaling cascade pathways and direct cancer association between miRNAs and mRNAs. Functional annotation and gene regulatory information can be directly retrieved from our web server, which can help users quickly identify significant interaction sub-network and report possible disease or cancer association. The tool can identify pivotal miRNAs or mRNAs that contribute to the complexity of cancer, while engaging modern next-generation sequencing technology to analyze the tumor and normal samples concurrently. We compared our tools with other visualization tools.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusion<\/jats:title>\n<jats:p>Our <jats:italic>MMiRNA-Viewer<\/jats:italic><jats:sup><jats:italic>2<\/jats:italic><\/jats:sup> serves as a multitasking platform in which users can identify significant interaction clusters and retrieve functional and cancer-associated information for miRNA-mRNA pairs between tumor and normal samples. Our tool is applicable across a range of diseases and cancers and has advantages over existing tools.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12859-020-3436-7","type":"journal-article","created":{"date-parts":[[2020,7,6]],"date-time":"2020-07-06T10:02:58Z","timestamp":1594029778000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["MMiRNA-Viewer2, a bioinformatics tool for visualizing functional annotation for MiRNA and MRNA pairs in a network"],"prefix":"10.1186","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9944-5426","authenticated-orcid":false,"given":"Yongsheng","family":"Bai","sequence":"first","affiliation":[]},{"given":"Steve","family":"Baker","sequence":"additional","affiliation":[]},{"given":"Kevin","family":"Exoo","sequence":"additional","affiliation":[]},{"given":"Xingqin","family":"Dai","sequence":"additional","affiliation":[]},{"given":"Lizhong","family":"Ding","sequence":"additional","affiliation":[]},{"given":"Naureen Aslam","family":"Khattak","sequence":"additional","affiliation":[]},{"given":"Hongtao","family":"Li","sequence":"additional","affiliation":[]},{"given":"Hannah","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Xiaoming","family":"Liu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,7,6]]},"reference":[{"issue":"15","key":"3436_CR1","doi-asserted-by":"crossref","first-page":"2161","DOI":"10.1038\/onc.2010.59","volume":"29","author":"ME Peter","year":"2010","unstructured":"Peter ME. 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