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Setting Up an Intronic miRNA Database

  • Ludwig Christian HinskeEmail author
  • Jens Heyn
  • Pedro A. F. Galante
  • Lucila Ohno-Machado
  • Simone Kreth
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 936)

Abstract

In the recent past, intragenic microRNAs (miRNAs) have gained significant attention. Due to the unique linkage to their host gene’s transcription, these miRNAs offer more information than intergenic miRNAs as they associate with some of their hosts’ properties. However, genome wide analysis of intronic miRNA data can be very challenging, especially if it relies on Web-based tools only. We therefore describe in this chapter how to set a database and how to link the different publicly available information resources on miRNAs and host genes. We also provide an example of a simple, but useful analysis technique. The basic structures and ideas suggested in this chapter can easily be extended to integrating other data and be applied to different analysis techniques.

Key words

Intronic miRNAs miRNA bioinformatics Biological databases miRBase bioinformatics Information retrieval Kyoto encyclopedia of genes and genomes analysis Gene ontology analysis 

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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Ludwig Christian Hinske
    • 1
    Email author
  • Jens Heyn
    • 2
  • Pedro A. F. Galante
    • 3
  • Lucila Ohno-Machado
    • 4
  • Simone Kreth
    • 2
  1. 1.Department of AnaesthesiologyClinic of the University of MunichMunichGermany
  2. 2.Clinic of AnesthesiologyClinic of the University of MunichMunichGermany
  3. 3.Laboratory of BioinformaticsInstituto de Ensino e Pesquisa—Hospital Sírio-LibanêsSão PauloBrazil
  4. 4.Division of Biomedical Informatics and TechnologyUniversity of California San DiegoLa JollaUSA

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