Skip to main content
SpringerLink
Log in

miRWalk Database for miRNA–Target Interactions

  • Protocol
  • First Online:
RNA Mapping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1182))

Abstract

miRWalk (http://mirwalk.uni-hd.de/) is a publicly available comprehensive resource, hosting the predicted as well as the experimentally validated microRNA (miRNA)–target interaction pairs. This database allows obtaining the possible miRNA-binding site predictions within the complete sequence of all known genes of three genomes (human, mouse, and rat). Moreover, it also integrates many novel features such as a comparative platform of miRNA-binding sites resulting from ten different prediction datasets, a holistic view of genetic networks of miRNA–gene pathway, and miRNA–gene–Online Mendelian Inheritance in Man disorder interactions, and unique experimentally validated information (e.g., cell lines, diseases, miRNA processing proteins). In this chapter, we describe a schematic workflow on how one can access the stored information from miRWalk and subsequently summarize its applications.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  PubMed  Google Scholar 

  2. Kim DH, Saetrom P, Snove O Jr et al (2008) MicroRNA-directed transcriptional gene silencing in mammalian cells. Proc Natl Acad Sci U S A 105:16230–16235

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  3. Lai EC (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30:363–364

    Article  CAS  PubMed  Google Scholar 

  4. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152–D157

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854

    Article  CAS  PubMed  Google Scholar 

  6. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20

    Article  CAS  PubMed  Google Scholar 

  7. Enright AJ, John B, Gaul U et al (2003) MicroRNA targets in Drosophila. Genome Biol 5:R1

    Article  PubMed Central  PubMed  Google Scholar 

  8. Krek A, Grun D, Poy MN et al (2005) Combinatorial microRNA target predictions. Nat Genet 37:495–500

    Article  CAS  PubMed  Google Scholar 

  9. Kertesz M, Iovino N, Unnerstall U et al (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39:1278–1284

    Article  CAS  PubMed  Google Scholar 

  10. Miranda KC, Huynh T, Tay Y et al (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126:1203–1217

    Article  CAS  PubMed  Google Scholar 

  11. Kiriakidou M, Nelson PT, Kouranov A et al (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18:1165–1178

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Wang X (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14:1012–1017

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  13. Rehmsmeier M, Steffen P, Hochsmann M et al (2004) Fast and effective prediction of micro RNA/target duplexes. RNA 10:1507–1517

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Vergoulis T, Vlachos IS, Alexiou P et al (2012) TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 40:D222–D229

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  15. Hsu SD, Lin FM, Wu WY et al (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 39:D163–D169

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Ruepp A, Kowarsch A, Schmidl D et al (2010) PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol 11: R6.

    Google Scholar 

  17. Jiang Q, Wang Y, Hao Y et al (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37:D98–D104

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  18. Dweep H, Sticht C, Gretz N (2013) In-silico algorithms for the screening of possible microRNA binding sites and their interactions. Curr Genomics 14:127–136

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Guang S, Bochner AF, Pavelec DM et al (2008) An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321:537–541

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  20. Lytle JR, Yario TA, Steitz JA (2007) Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc Natl Acad Sci U S A 104: 9667–9672

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Place RF, Li LC, Pookot D et al (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A 105:1608–1613

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  22. Tay Y, Zhang J, Thomson AM et al (2008) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455:1124–1128

    Article  CAS  PubMed  Google Scholar 

  23. Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38:S8–S13

    Article  CAS  PubMed  Google Scholar 

  24. Dweep H, Sticht C, Pandey P et al (2011) miRWalk – database: prediction of possible miRNA binding sites by “walking” the genes of three genomes. J Biomed Inform 44: 839–847

    Article  CAS  PubMed  Google Scholar 

  25. Kanehisa M, Goto S, Kawashima S et al (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30:42–46

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Dong J, Jiang G, Asmann YW et al (2010) MicroRNA networks in mouse lung organogenesis. PLoS One 5:e10854

    Article  PubMed Central  PubMed  Google Scholar 

  27. Ucar A, Vafaizadeh V, Jarry H et al (2010) miR-212 and miR-132 are required for epithelial stromal interactions necessary for mouse mammary gland development. Nat Genet 42: 1101–1108

    Article  CAS  PubMed  Google Scholar 

  28. Ikemura K, Yamamoto M, Miyazaki S et al (2013) MicroRNA-145 post-transcriptionally regulates the expression and function of P-glycoprotein in intestinal epithelial cells. Mol Pharmacol 83:399–405

    Article  CAS  PubMed  Google Scholar 

  29. Ho J, Ng KH, Rosen S et al (2008) Podocyte-specific loss of functional microRNAs leads to rapid glomerular and tubular injury. J Am Soc Nephrol 19:2069–2075

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Shi S, Yu L, Chiu C et al (2008) Podocyte-selective deletion of dicer induces proteinuria and glomerulosclerosis. J Am Soc Nephrol 19: 2159–2169

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Dweep H, Sticht C, Kharkar A et al (2013) Parallel analysis of mRNA and microRNA microarray profiles to explore functional regulatory patterns in polycystic kidney disease: using PKD/Mhm rat model. PLoS One 8: e53780

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  32. Cirera-Salinas D, Pauta M, Allen RM et al (2012) Mir-33 regulates cell proliferation and cell cycle progression. Cell Cycle 11:922–933

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  33. Wulfken LM, Moritz R, Ohlmann C et al (2011) MicroRNAs in renal cell carcinoma: diagnostic implications of serum miR-1233 levels. PLoS One 6:e25787

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  34. Zhao C, Huang C, Weng T et al (2012) Computational prediction of MicroRNAs targeting GABA receptors and experimental verification of miR-181, miR-216 and miR-203 targets in GABA-A receptor. BMC Res Notes 5:91

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  35. Papagregoriou G, Erguler K, Dweep H et al (2012) A miR-1207-5p binding site polymorphism abolishes regulation of HBEGF and is associated with disease severity in CFHR5 nephropathy. PLoS ONE 7:e31021

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  36. Felekkis K, Voskarides K, Dweep H et al (2011) Increased number of microRNA target sites in genes encoded in CNV regions. Evidence for an evolutionary genomic interaction. Mol Biol Evol 28:2421–2424

    Article  CAS  PubMed  Google Scholar 

  37. Durand C, Roeth R, Dweep H et al (2011) Alternative splicing and nonsense-mediated RNA decay contribute to the regulation of SHOX expression. PLoS One 6:e18115

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  38. Bandiera S, Ruberg S, Girard M et al (2011) Nuclear outsourcing of RNA interference components to human mitochondria. PLoS One 6:e20746

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  39. Xu LM, Li JR, Huang Y et al (2012) AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic Acids Res 40:D1016–D1022

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  40. Santamaria C, Muntion S, Roson B et al (2012) Impaired expression of DICER, DROSHA, SBDS and some microRNAs in mesenchymal stromal cells from myelodysplastic syndrome patients. Haematologica 97:1218–1224

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgements

This work is funded by the Research Council through Graduiertenkolleg 886 and by the German Federal Ministry of Research and Education through the National Genome Research Network (NGFN-2, Grant no. 01GR 0450).

Author information

Authors and Affiliations

  1. Medical Faculty Mannheim, Medical Research Center, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, D-68167, Mannheim, Germany

    Harsh Dweep Ph.D., Norbert Gretz & Carsten Sticht

Authors
  1. Harsh Dweep Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Norbert Gretz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Carsten Sticht
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Harsh Dweep Ph.D. .

Editor information

Editors and Affiliations

  1. Diabetes, Cardiovascular, and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, Arizona, USA

    M. Lucrecia Alvarez

  2. Department of Plastic Surgery, University Hospital of the RWTH Aachen, Germany

    Mahtab Nourbakhsh

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media New York

About this protocol

Cite this protocol

Dweep, H., Gretz, N., Sticht, C. (2014). miRWalk Database for miRNA–Target Interactions. In: Alvarez, M., Nourbakhsh, M. (eds) RNA Mapping. Methods in Molecular Biology, vol 1182. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1062-5_25

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-1062-5_25

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1061-8

  • Online ISBN: 978-1-4939-1062-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation