Hamzeiy Hamid, Suluyayla Rabia, Brinkrolf Christoph, Janowski Sebastian Jan, Hofestaedt Ralf, Allmer Jens
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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.
微小RNA（miRNA）是已知参与基因表达转录后调控的小RNA分子。在此，VANESA这个现有的用于重建、可视化和分析大型生物网络的平台已进一步扩展，纳入了miRBase、TarBase和miRTarBase中所有经过实验验证的人类miRNA。这是通过将一个定制的混合miRNA数据库整合到VANESA的主要数据源DAWIS - M.D.中来实现的，从而能够在大型生物途径（如京都基因与基因组百科全书（KEGG）中发现的途径）中对miRNA进行可视化和分析。有趣的是，99.15%的人类KEGG途径要么包含被miRNA靶向的基因，要么含有miRNA。这主要是由于每个miRNA可能具有大量的相互作用伙伴（例如：hsa - miR - 335 - 5p靶向2544个基因，71个miRNA靶向NUFIP2）。我们通过分析麻疹病毒KEGG途径作为原理验证模型来证明我们系统的可用性，并进一步强调将miRNA（包括经过实验验证的和预测的）整合到生物网络中对于阐明具有生物学重要性的新型miRNA - mRNA相互作用的重要性。
