Setting Up an Intronic miRNA Database

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


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 


  1. 1.
    Lin S-L, Miller JD, Ying S-Y (2006) Intronic microRNA (miRNA). J Biomed Biotechnol 2006(4):26818PubMedGoogle Scholar
  2. 2.
    Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res 14(10A):1902–1910PubMedCrossRefGoogle Scholar
  3. 3.
    Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L (2010) A potential role for intragenic miRNAs on their hosts’ interactome. BMC Genomics 11:533PubMedCrossRefGoogle Scholar
  4. 4.
    Kim Y-K, Kim VN (2007) Processing of intronic microRNAs. EMBO J 26(3): 775–783PubMedCrossRefGoogle Scholar
  5. 5.
    Morlando M, Ballarino M, Gromak N, Pagano F, Bozzoni I, Proudfoot N (2008) Primary microRNA transcripts are processed co-transcriptionally. Nat Struct Mol Biol 15:902–909PubMedCrossRefGoogle Scholar
  6. 6.
    Xiong H, Qian J, He T, Li F (2009) Independent transcription of miR-281 in the intron of ODA in Drosophila melanogaster. Biochem Biophys Res Commun 378(4): 883–889PubMedCrossRefGoogle Scholar
  7. 7.
    Baskerville S, Bartel DP (2005) Microarray profiling of microRNAs reveals frequent ­coexpression with neighboring miRNAs and host genes. RNA 11(3):241–247PubMedCrossRefGoogle Scholar
  8. 8.
    Li S-C, Tang P, Lin W-C (2007) Intronic microRNA: discovery and biological implications. DNA Cell Biol 26(4):195–207PubMedCrossRefGoogle Scholar
  9. 9.
    Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M et al (2010) miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res 38(Database issue):D137–D141Google Scholar
  10. 10.
    Griffiths-Jones S (2004) The microRNA registry. Nucleic Acids Res 32(Database issue): D109–D111Google Scholar
  11. 11.
    Griffiths-Jones S, Grocock RJ, Van Dongen S, Bateman A, Enright AJ (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 34(Database issue):D140–D144Google Scholar
  12. 12.
    Griffiths-Jones S (2006) miRBase: the microRNA sequence database. Methods Mol Biol 342:129–138PubMedGoogle Scholar
  13. 13.
    Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36(Database issue):D154–D158Google Scholar
  14. 14.
    Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG (2007) miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res 35(Database issue):D149–D155Google Scholar
  15. 15.
    Lee C, Alekseyenko A, Brown CT (eds) (2009) Exploring the future of bioinformatics data sharing and mining with Pygr and Worldbase. Proceedings of the 8th Python in Science Conference. Pasadena, CA, USAGoogle Scholar
  16. 16.
    Gentleman R, Ihaka R (1997) The R language. Comput Sci Stat 28:326–330Google Scholar
  17. 17.
    Gentleman R, Carey V, Dudoit S, Ellis B, Gautier L (2003) The bioconductor project. bepresscomGoogle Scholar
  18. 18.
    Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5(10):R80PubMedCrossRefGoogle Scholar
  19. 19.
    Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33(Database issue):D501–D504Google Scholar
  20. 20.
    Karolchik D, Hinrichs AS, Kent WJ (2009) The UCSC genome browser. Curr Protoc Bioinformatics Chapter 1:Unit1.4Google Scholar
  21. 21.
    Mangan ME, Williams JM, Kuhn RM, Lathe WC (2009) The UCSC genome browser: what every molecular biologist should know. Curr Protoc Mol Biol Chapter 19:Unit19.9Google Scholar
  22. 22.
    Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M et al (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36(Database issue):D480–D484Google Scholar
  23. 23.
    Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30PubMedCrossRefGoogle Scholar
  24. 24.
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29PubMedCrossRefGoogle Scholar
  25. 25.
    John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS (2004) Human microRNA targets. PLoS Biol 2(11):e363PubMedCrossRefGoogle Scholar
  26. 26.
    Lewis BP, I-h S, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115(7):787–798PubMedCrossRefGoogle Scholar
  27. 27.
    Doench JG, Petersen CP, Sharp PA (2003) siRNAs can function as miRNAs. Genes Dev 17(4):438–442PubMedCrossRefGoogle Scholar
  28. 28.
    Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39(10):1278–1284PubMedCrossRefGoogle Scholar
  29. 29.
    Zhang J, Carey V, Gentleman R (2003) An extensible application for assembling annotation for genomic data. Bioinformatics 19:155–156PubMedCrossRefGoogle Scholar

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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