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

BMC Proceedings

Jinwook Seo¹  Eric Hoffman²  Mamta Giri³  Robert J Freishtat²  Bohyoung Kim⁴  Daekyoung Jung¹ 

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

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

Others  :  1222586
DOI  :  10.1186/1753-6561-9-S6-S2

【 摘 要 】

Background

MicroRNAs (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.

Results

We 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 webcite.

Conclusions

We 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】

   
2015 Jung et al.

【 图 表 】

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