Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA

J Integr Bioinform. 2017 Jun 13;14(1):20160004. doi: 10.1515/jib-2016-0004.


MicroRNAs (miRNAs) are small RNA molecules which are known to take part in post-transcriptional regulation of gene expression. Here, VANESA, an existing platform for reconstructing, visualizing, and analysis of large biological networks, has been further expanded to include all experimentally validated human miRNAs available within miRBase, TarBase and miRTarBase. This is done by integrating a custom hybrid miRNA database to DAWIS-M.D., VANESA's main data source, enabling the visualization and analysis of miRNAs within large biological pathways such as those found within the Kyoto Encyclopedia of Genes and Genomes (KEGG). Interestingly, 99.15 % of human KEGG pathways either contain genes which are targeted by miRNAs or harbor them. This is mainly due to the high number of interaction partners that each miRNA could have (e.g.: hsa-miR-335-5p targets 2544 genes and 71 miRNAs target NUFIP2). We demonstrate the usability of our system by analyzing the measles virus KEGG pathway as a proof-of-principle model and further highlight the importance of integrating miRNAs (both experimentally validated and predicted) into biological networks for the elucidation of novel miRNA-mRNA interactions of biological importance.

Keywords: KEGG pathway; VANESA; measles; microRNA; target database.

MeSH terms

  • Databases, Genetic
  • Gene Expression Regulation / genetics
  • Gene Regulatory Networks / genetics*
  • Genes*
  • Genome / genetics*
  • Humans
  • Japan
  • MicroRNAs / analysis*
  • MicroRNAs / genetics*
  • Nuclear Proteins / genetics
  • RNA, Messenger / genetics
  • RNA-Binding Proteins / genetics
  • Reproducibility of Results


  • MIRN335 microRNA, human
  • MicroRNAs
  • NUFIP2 protein, human
  • Nuclear Proteins
  • RNA, Messenger
  • RNA-Binding Proteins