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

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.

[1]  Tsviya Olender,et al.  GeneCards Version 3: the human gene integrator , 2010, Database J. Biol. Databases Curation.

[2]  Juan Liu,et al.  A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules , 2011, Bioinform..

[3]  Edward M. Reingold,et al.  Graph drawing by force‐directed placement , 1991, Softw. Pract. Exp..

[4]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[5]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[6]  Curtis Balch,et al.  MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression , 2009, Nucleic Acids Res..

[7]  Anjali J. Koppal,et al.  Supplementary data: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites , 2010 .

[8]  A. Kraskov,et al.  Erratum: Estimating mutual information [Phys. Rev. E 69, 066138 (2004)] , 2011 .

[9]  A. Kraskov,et al.  Estimating mutual information. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[10]  B. Frey,et al.  Using expression profiling data to identify human microRNA targets , 2007, Nature Methods.

[11]  Cesare Furlanello,et al.  minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers , 2012, Bioinform..

[12]  A. Ballabio,et al.  MicroRNA target prediction by expression analysis of host genes. , 2009, Genome research.

[13]  Xiaowei Wang.  miRDB: a microRNA target prediction and functional annotation database with a wiki interface. , 2008, RNA.

[14]  Bernd Meyer,et al.  Self-Organizing Graphs - A Neural Network Perspective of Graph Layout , 1998, GD.

[15]  Yong E. Zhang,et al.  A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes , 2011, Bioinform..

[16]  Yadong Wang,et al.  miR2Disease: a manually curated database for microRNA deregulation in human disease , 2008, Nucleic Acids Res..

[17]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[18]  Nectarios Koziris,et al.  DIANA-microT web server: elucidating microRNA functions through target prediction , 2009, Nucleic Acids Res..

[19]  Michael Mitzenmacher,et al.  Detecting Novel Associations in Large Data Sets , 2011, Science.

[20]  Satoru Kawai,et al.  An Algorithm for Drawing General Undirected Graphs , 1989, Inf. Process. Lett..

[21]  Robert J Freishtat,et al.  Adipocyte-derived Exosomal miRNAs: A Novel Mechanism for Obesity-Related Disease , 2014, Pediatric Research.

[22]  Panayiotis V. Benos,et al.  mirConnX: condition-specific mRNA-microRNA network integrator , 2011, Nucleic Acids Res..

[23]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[24]  Anton J. Enright,et al.  MicroRNA targets in Drosophila , 2003, Genome Biology.

[25]  Gabriele Sales,et al.  MAGIA2: from miRNA and genes expression data integrative analysis to microRNA–transcription factor mixed regulatory circuits (2012 update) , 2012, Nucleic Acids Res..