Visualization and analysis of miRNAs implicated in amyotrophic lateral sclerosis within gene regulatory pathways

Abstract

MicroRNAs (miRNAs), approximately 22 nucleotides long, post-transcriptionally active gene expression regulators, play active roles in modulating cellular processes. Gene regulation and miRNA regulation are intertwined and the main aim of this study is to facilitate the analysis of miRNAs within gene regulatory pathways. VANESA enables the reconstruction of biological pathways and supports visualization and simulation. To support integrative miRNA and gene pathway analyses, a custom database of experimentally proven miRNAs, integrating data from miRBase, TarBase and miRTarBase, was added to DAWIS-M.D., which is the main data source for VANESA. Analysis of human KEGG pathways within DAWIS-M.D. showed that 661 miRNAs (~1/3 recorded human miRNAs) lead to 65,474 interactions. hsa-miR-335-5p targets most genes in our system (2,544); while the most targeted gene (with 71 miRNAs) is NUFIP2 (Nuclear Fragile X Mental Retardation Protein Interacting Protein 2). Amyotrophic Lateral Sclerosis (ALS), a complex neurodegenerative disease, was chosen as a proof of concept model. Using our system, it was possible to reduce the initially several hundred genes and miRNAs associated with ALS to eight genes, 19 miRNAs and 31 interactions. This highlights the effectiveness of the implemented system to distill important information from otherwise hard to access, highly convoluted and vast regulatory networks.