title: Visual Display of 5p-arm and 3p-arm miRNA Expression with a Mobile Application.
abstract: MicroRNAs (miRNAs) play important roles in human cancers. In previous studies, we have demonstrated that both 5p-arm and 3p-arm of mature miRNAs could be expressed from the same precursor and we further interrogated the 5p-arm and 3p-arm miRNA expression with a comprehensive arm feature annotation list. To assist biologists to visualize the differential 5p-arm and 3p-arm miRNA expression patterns, we utilized a user-friendly mobile App to display. The Cancer Genome Atlas (TCGA) miRNA-Seq expression information. We have collected over 4,500 miRNA-Seq datasets from 15 TCGA cancer types and further processed them with the 5p-arm and 3p-arm annotation analysis pipeline. In order to be displayed with the RNA-Seq Viewer App, annotated 5p-arm and 3p-arm miRNA expression information and miRNA gene loci information were converted into SQLite tables. In this distinct application, for any given miRNA gene, 5p-arm miRNA is illustrated on the top of chromosome ideogram and 3p-arm miRNA is illustrated on the bottom of chromosome ideogram. Users can then easily interrogate the differentially 5p-arm/3p-arm expressed miRNAs with their mobile devices. This study demonstrates the feasibility and utility of RNA-Seq Viewer App in addition to mRNA-Seq data visualization.
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Chao-Yu
authors.initials: CY
authors.lastname: Pan
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan.
authors.forename: Wei-Ting
authors.initials: WT
authors.lastname: Kuo
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
authors.forename: Chien-Yuan
authors.initials: CY
authors.lastname: Chiu
authors.affiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan; Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 112, Taiwan.
authors.forename: Wen-Chang
authors.identifier: 0000-0003-0194-1745
authors.initials: WC
authors.lastname: Lin
mesh_terms: D030541:Databases, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020407:Internet; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D063731:Mobile Applications; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs