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Project Members:

• Marcos J Arauzo-Bravo (admin)

[Marcos J Arauzo-Bravo]

miRDiana: Consensus serach of miRs targeting a list of genes

Marcos J. Araúzo-Bravo
mararabra@yahoo.co.uk

• Computational Biology and Bioinformatics Group, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany;
• Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014 San Sebastián, Spain
• Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
• IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain

INTRODUCTION

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miRDiana is a software package developed software in MATLAB® (MathWorks®) to
search for select miRNA target genes.
miRDiana that collects the union of mouse validated targets from the TargetScan (Agarwal ey al, 2015),
MicroCosm (Griffiths-Jones et al, 2008), mirTarBase (Chou et al, 2006) and miRWalk 2.0 (Dweep and Gretz, 2017) databases.

Among other works miRDiana have been applied to search for miRNAs targeting Brca1 in Gerovska et al, 2020.

METHOD

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Firstly, the software downloads each database and preprocesses by standardizing the miRNA and gene names.

1. It strips the miRNA names from the species ids and converts the gene names to the official symbols of the National Center for Biotechnology Information (NCBI) database.
2. Next, for each potential gene target it calculates an incidence matrix with all the miRNAs of each database targeting such gene.
3. Finally, it builds a consensus matrix with the cases of the appearance of each miRNA in the four analyzed miRNA databases.

REFERENCES

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Gerovska, D,: Larrinaga, G.; Solano-Iturri, JD.; Márquez, J.; García Gallastegi, P.; Khatib, A.M.; Poschmann, G.; Stühler, K.; Armesto, M.; Lawrie, C.H.; Badiola, I.; Araúzo-Bravo, M.J.
An integrative omics approach reveals involvement of BRCA1 in the hepatic metastatic progression of colorectal cancer. Cancers. In press, 2020.

Agarwal, V.; Bell, G.W.; Nam, J.; Bartel, D.P.
Predicting effective microRNA target sites in mammalian mRNAs. eLife. 2015, 4, e05005.

Griffiths-Jones, S.; Saini, H.K.; van Dongen, S.; Enright, A.J.
miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008, 36(Database issue), D154-D158.

Chou, C.H.; Chang, N.W.; Shrestha, S.; Hsu, S.D.; Lin, Y.L.; Lee, W.H.; Yang, C.D.; Hong, H.C.; Wei, T.Y.; Tu, S.J.; et al.
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res. 2016, 44, D239-D247.

Dweep, H.; Gretz, N.
miRWalk2.0: a comprehensive atlas of microRNA-target interactions. Nat Methods. 2015, 12, 697.