miRTarVis: an interactive visual analysis tool for microRNA-mRNA expression profile data

BMC Proceedings

Research

Mamta Giri¹  Eric Hoffman²  Daekyoung Jung³  Jinwook Seo³  Bohyoung Kim⁴  Robert J Freishtat⁵ 

[1] Center for Genetic Medicine Research, Children's National Medical Center, Washington, D.C., USA;Center for Genetic Medicine Research, Children's National Medical Center, Washington, D.C., USA;Department of Integrative Systems Biology, George Washington University, 111 Michigan Avenue, NW, 20010-2970, Washington, D.C., USA;Department of Computer Science and Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, South Korea;Department of Radiology, Seoul National University Bundang Hospital, 300 Gumi-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, South Korea;Division of Emergency Medicine, Children's National Medical Center, Washington, D.C., USA;Center for Genetic Medicine Research, Children's National Medical Center, Washington, D.C., USA;Department of Integrative Systems Biology, George Washington University, 111 Michigan Avenue, NW, 20010-2970, Washington, D.C., USA;

关键词: MicroRNA;    mRNA;    Visualization;    Expression profile;    Target prediction;   

DOI  :  10.1186/1753-6561-9-S6-S2

来源: Springer

【 摘 要 】

BackgroundMicroRNAs (miRNA) are short nucleotides that down-regulate its target genes. Various miRNA target prediction algorithms have used sequence complementarity between miRNA and its targets. Recently, other algorithms tried to improve sequence-based miRNA target prediction by exploiting miRNA-mRNA expression profile data. Some web-based tools are also introduced to help researchers predict targets of miRNAs from miRNA-mRNA expression profile data. A demand for a miRNA-mRNA visual analysis tool that features novel miRNA prediction algorithms and more interactive visualization techniques exists.ResultsWe designed and implemented miRTarVis, which is an interactive visual analysis tool that predicts targets of miRNAs from miRNA-mRNA expression profile data and visualizes the resulting miRNA-target interaction network. miRTarVis has intuitive interface design in accordance with the analysis procedure of load, filter, predict, and visualize. It predicts targets of miRNA by adopting Bayesian inference and MINE analyses, as well as conventional correlation and mutual information analyses. It visualizes a resulting miRNA-mRNA network in an interactive Treemap, as well as a conventional node-link diagram. miRTarVis is available at http://hcil.snu.ac.kr/~rati/miRTarVis/index.html.ConclusionsWe reported findings from miRNA-mRNA expression profile data of asthma patients using miRTarVis in a case study. miRTarVis helps to predict and understand targets of miRNA from miRNA-mRNA expression profile data.

【 授权许可】

Unknown   
© Jung et al. 2015. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.