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Visual Display of 5p-arm and 3p-arm miRNA Expression with a Mobile Application.

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 l...

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Published in:BioMed Research International Vol. 2017; pp. 1 - 8
Main Authors: Pan, Chao-Yu, Kuo, Wei-Ting, Chiu, Chien-Yuan, Lin, Wen-chang
Format: pictorial research tables/charts Journal Article
Published: Wiley-Blackwell 2/8/2017
Online Access:View this record in EBSCOhost
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      jtl: BioMed Research International
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      dt: 2/8/2017
      vid: 2017
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      pub: Wiley-Blackwell
      place: Malden, Massachusetts
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        10.1155/2017/6037168
        121185194
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        atl: Visual Display of 5p-arm and 3p-arm miRNA Expression with a Mobile Application.
      aug:
        au:
          Pan, Chao-Yu
          Kuo, Wei-Ting
          Chiu, Chien-Yuan
          Lin, Wen-chang
        affil: Institute of Biomedical Informatics, National Yang-Ming University, Taipei 112, Taiwan
      sug:
        subj:
          Gene Expression
          Mobile Applications
          Data Display
          Neoplasms Familial and Genetic
          Chromosomes
          Human
          RNA
          Funding Source
      ab: 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.
      pubtype: Academic Journal
      doctype:
        pictorial
        research
        tables/charts
        Journal Article
      ougenre: Article
    language: English
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