Article
VANESA, facilitating the integrated analysis of gene and microRNA-based regulation
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Authors
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Christoph Brinkrolf
- Department of Bioinformatics and Medical Informatics, Faculty of Technology, Bielefeld University, Bielefeld, Deutschland
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Ralf Hofestaedt
- Department of Bioinformatics and Medical Informatics, Faculty of Technology, Bielefeld University, Bielefeld, Deutschland
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Jens Allmer
- Applied Bioinformatics, Wageningen University and Research, BU Bioscience, Wageningen, Netherlands
| Published: | August 27, 2018 |
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Outline
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Introduction: A disease often manifests itself through protein dysregulation. MicroRNAs (miRNAs) are involved in the post-transcriptional regulation of protein abundance. Therefore, they have often been implicated with human disease. These approximately 22 nucleotides long, non-coding RNAs play active roles in fine tuning cellular processes. Currently, gene regulatory pathways are employed to analyze diseases using, for example, transcriptomics data. Current pathways as available on Reactome and KEGG, lack miRNA-based interactions and only model transcriptional gene regulation.
Methods: We adapted VANESA, a tool which enables the reconstruction of biological pathways and supports visualization, and simulation, to allow the integration of miRNAs into available pathways. Thereby, we were able to annotated the Measels and ALS pathways with miRNAs originating from genes and/or targeting genes in the respective pathways. MicroRNAs and their targets were curated into an integrated resources from miRBase, TarBase and miRTarBase.
Results: Here we detail how an integrated analysis of miRNA-bases and gene-based regulation can be performed with VANESA. The workflow will enable anyone to investigate integrated miRNA and gene regulation in human.
Discussion: This will help shed new light on disease mechanisms.
The authors declare that they have no competing interests.
The authors declare that an ethics committee vote is not required.
