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.
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References
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
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
Lai EC (2002) Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30:363–364
Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152–D157
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
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
Enright AJ, John B, Gaul U et al (2003) MicroRNA targets in Drosophila. Genome Biol 5:R1
Krek A, Grun D, Poy MN et al (2005) Combinatorial microRNA target predictions. Nat Genet 37:495–500
Kertesz M, Iovino N, Unnerstall U et al (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39:1278–1284
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
Kiriakidou M, Nelson PT, Kouranov A et al (2004) A combined computational-experimental approach predicts human microRNA targets. Genes Dev 18:1165–1178
Wang X (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14:1012–1017
Rehmsmeier M, Steffen P, Hochsmann M et al (2004) Fast and effective prediction of micro RNA/target duplexes. RNA 10:1507–1517
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
Hsu SD, Lin FM, Wu WY et al (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 39:D163–D169
Ruepp A, Kowarsch A, Schmidl D et al (2010) PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol 11: R6.
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
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
Guang S, Bochner AF, Pavelec DM et al (2008) An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321:537–541
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
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
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
Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38:S8–S13
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
Kanehisa M, Goto S, Kawashima S et al (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30:42–46
Dong J, Jiang G, Asmann YW et al (2010) MicroRNA networks in mouse lung organogenesis. PLoS One 5:e10854
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
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
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
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
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
Cirera-Salinas D, Pauta M, Allen RM et al (2012) Mir-33 regulates cell proliferation and cell cycle progression. Cell Cycle 11:922–933
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
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
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
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
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
Bandiera S, Ruberg S, Girard M et al (2011) Nuclear outsourcing of RNA interference components to human mitochondria. PLoS One 6:e20746
Xu LM, Li JR, Huang Y et al (2012) AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic Acids Res 40:D1016–D1022
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
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).
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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
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DOI: https://doi.org/10.1007/978-1-4939-1062-5_25
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