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Prediction of miRNA–mRNA Interactions Using miRGate

  • Eduardo Andrés-León
  • Gonzalo Gómez-López
  • David G. Pisano
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1580)

Abstract

miRGate (http://mirgate.bioinfo.cnio.es/) is a freely available database that contains predicted and experimentally validated microRNA–messenger RNA (miRNA–mRNA) target pairs. This resource includes novel predictions from five well-established algorithms, but recalculated from a common and comprehensive sequence dataset. It includes all 3′-UTR sequences of all known genes of the three more widely employed genomes (human, mouse, and rat), and all annotated miRNA sequences from those genomes. Besides, it also contains predictions for all genes in human targeted by miRNA viruses such as Epstein-Barr and Kaposi sarcoma-associated herpes virus.

The approach intends to circumvent one of the main drawbacks in this area, as diverse sequences and gene database versions cause poor overlap among different target prediction methods even with experimentally confirmed targets. As a result, miRGate predictions have been successfully validated using functional assays in several laboratories.

This chapter describes how a user can access target information via miRGate’s web interface. It also shows how automatically access the database through the programmatic interface based on representational state transfer services (REST), using the application programming interface (API) available at http://mirgate.bioinfo.cnio.es/API.

Key words

MicroRNA Prediction 3′-UTR Validated API Target site 

Notes

Acknowledgments

The authors would like to thank to Rocio Nuñez for critical reading of the manuscript.

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Eduardo Andrés-León
    • 1
  • Gonzalo Gómez-López
    • 2
  • David G. Pisano
    • 2
  1. 1.Bioinformatics UnitInstituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), PTS GranadaGranadaSpain
  2. 2.Bioinformatics Unit (UBio), Structural Biology and Biocomputing ProgrammeSpanish National Cancer Research Centre (CNIO)MadridSpain

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