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, researchers at the National Yang-Ming University 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, they utilized a user-friendly mobile App to display the Cancer Genome Atlas (TCGA) miRNA-Seq expression information. They 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.

RNA-Seq Viewer display (overall chromosome view)

rna-seqHuman gene expression information is displayed with the RNA-Seq Viewer App. Sample information and navigation panel are located at the bottom section. Tumor tissue expression is illustrated with light-red color lines and normal tissue expression background is illustrated with light-green color lines.

Availability – The RNA_Seq Viewer App can be obtained freely through Apple iTune App Store (https://itunes.apple.com/us/app/rna-seq-viewer/id898456094?mt=8).

Pan CY, Kuo WT, Chiu CY, Lin WC. (2017) Visual Display of 5p-arm and 3p-arm miRNA Expression with a Mobile Application. Biomed Res Int 2017:6037168. [article]

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.