MiRWalk database for miRNA-target interactions

Methods in Molecular Biology

Volumn 1182, Issue , 2014, Pages 289-305

  Dweep, Harsh ^a   Gretz, Norbert ^a   Sticht, Carsten ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

3' UTR; 5' UTR; Application; CDS; MicroRNA; miRWalk; OMIM; Pathways; Prediction; Promoter; Validated

Indexed keywords

MICRORNA; MESSENGER RNA;

ARTICLE; DATA BASE; GENE TARGETING; GENOME; HUMAN; INHERITANCE; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RAT; WORKFLOW; ANIMAL; GENETIC DATABASE; GENETICS; METABOLISM; NUCLEIC ACID DATABASE;

ANIMALS; DATABASES, GENETIC; DATABASES, NUCLEIC ACID; HUMANS; MICRORNAS; RNA, MESSENGER;

EID: 84925883377     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1062-5_25     Document Type: Article

References (40)

1. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297
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
3. Lai EC (2002) Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-Transcriptional regulation. Nat Genet 30: 363-364
4. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39: D152-D157
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
6. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often fl anked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20
7. Enright AJ, John B, Gaul U et al (2003) MicroRNA targets in Drosophila. Genome Biol 5: R1
8. Krek A, Grun D, Poy MN et al (2005) Combinatorial microRNA target predictions. Nat Genet 37: 495-500
9. Kertesz M, Iovino N, Unnerstall U et al (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284
10. Miranda KC, Huynh T, Tay Y et al (2006) A pattern-based method for the identifi cation of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217
11. Kiriakidou M, Nelson PT, Kouranov A et al (2004) A combined computational- experimental approach predicts human microRNA targets. Genes Dev 18: 1165-1178
12. Wang X (2008) miRDB: a microRNA target prediction and functional annotation database with a wiki interface. RNA 14: 1012-1017
13. Rehmsmeier M, Steffen P, Hochsmann M et al (2004) Fast and effective prediction of micro RNA/target duplexes. RNA 10: 1507-1517
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
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
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
17. Jiang Q, Wang Y, Hao Y et al (2009) miR2-Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37: D98-D104
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
19. Guang S, Bochner AF, Pavelec DM et al (2008) An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321: 537-541
20. Lytle JR, Yario TA, Steitz JA (2007) Target mRNAs are repressed as effi ciently by microRNA-binding sites in the 5' UTR as in the 3' UTR. Proc Natl Acad Sci U S A 104: 9667-9672
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
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
23. Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38: S8-S13
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
25. Kanehisa M, Goto S, Kawashima S et al (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30: 42-46
26. Dong J, Jiang G, Asmann YW et al (2010) MicroRNA networks in mouse lung organogenesis. PLoS One 5: e10854
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
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
29. Ho J, Ng KH, Rosen S et al (2008) Podocytespecifi c loss of functional microRNAs leads to rapid glomerular and tubular injury. J Am Soc Nephrol 19: 2069-2075
30. Shi S, Yu L, Chiu C et al (2008) Podocyteselective deletion of dicer induces proteinuria and glomerulosclerosis. J Am Soc Nephrol 19: 2159-2169
31. Dweep H, Sticht C, Kharkar A et al (2013) Parallel analysis of mRNA and microRNA microarray profi les to explore functional regulatory patterns in polycystic kidney disease: using PKD/Mhm rat model. PLoS One 8: e53780
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
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
34. Zhao C, Huang C, Weng T et al (2012) Computational prediction of MicroRNAs targeting GABA receptors and experimental verifi cation of miR-181, miR-216 and miR-203 targets in GABA-A receptor. BMC Res Notes 5: 91
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
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
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
38. Bandiera S, Ruberg S, Girard M et al (2011) Nuclear outsourcing of RNA interference components to human mitochondria. PLoS One 6: e20746
39. Xu LM, Li JR, Huang Y et al (2012) AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic Acids Res 40: D1016-D1022
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