Identification of microRNA activity by targets' reverse expression

Bioinformatics

Volumn 26, Issue 1, 2009, Pages 91-97

  Volinia, Stefano ^a,b,c   Visone, Rosa ^c   Galasso, Marco ^a   Rossi, Elda ^d   Croce, Carlo M ^c  

^a UNIVERSITY OF FERRARA   (Italy)

^b OHIO STATE UNIVERSITY   (United States)

^c OHIO STATE UNIVERSITY   (United States)

^d CINECA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA;

EID: 75249096480     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp598     Document Type: Article

References (57)

1. Arora, A. and Simpson, D.A. (2008) Individual mRNA expression profiles reveal the effects of specific microRNAs. Genome Biol., 9, R82.
2. Baek, D. et al. (2008) The impact of microRNAs on protein output. Nature, 455, 64-71.
3. Barrett, T. et al. (2007) NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res., 35, D760-D765.
4. Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
5. Bemis, L.T. et al. (2008) MicroRNA-137 targets microphthalmia-associated transcription factor in melanoma cell lines. Cancer Res., 68, 1362-1368.
6. Bonci, D. et al. (2008) The miR-15a-miR-16-1 cluster controls prostate cancer by targeting multiple oncogenic activities. Nature Med., 14, 1271-1277.
7. Brohee, S. et al. (2008) Network Analysis Tools: from biological networks to clusters and pathways. Nature Protocols, 3, 1616-1629.
8. Brohee, S. and van Helden, J. (2006) Evaluation of clustering algorithms for protein interaction networks. BMC bioinformatics, 7, 488.
9. Calin, G.A. et al. (2008) MiR-15a and miR-16-1 cluster functions in human leukemia. Proc. Natl Acad. Sci. USA, 105, 5166-5171.
10. Calin, G.A. et al. (2005) A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. New Engl. J. Med., 353, 1793-1801.
11. Chang, T.C. et al. (2007) Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Molecular Cell, 26, 745-752.
12. Cheng, C. and Li, L.M. (2008) Inferring microRNA activities by combining gene expression with microRNA target prediction. PLoS ONE, 3, e1989.
13. Corney, D.C. et al. (2007) MicroRNA-34b and MicroRNA-34c are targets of p53 and cooperate in control of cell proliferation and adhesion-independent growth. Cancer Res., 67, 8433-8438.
14. Enright, A.J. et al. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
15. Fabbri, M. et al. (2007) MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc. Natl Acad. Sci. USA, 104, 15805-15810.
16. Farh, K.K. et al. (2005) The widespread impact of mammalian MicroRNAs on mRNA repression and evolution, Science, 310, 1817-1821.
17. Fornari, F. et al. (2008) MiR-221 controls CDKN1C/p57 and CDKN1B/p27 expression in human hepatocellular carcinoma, Oncogene, 27, 5651-5661.
18. Friedman, R.C. et al. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92-105.
19. Galan-Caridad, J.M. et al. (2007) Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell, 129, 345-357.
20. Galardi, S. et al. (2007) miR-221 and miR-222 expression affects the proliferation potential of human prostate carcinoma cell lines by targeting p27Kip1. J. Biol. Chem., 282, 23716-23724.
21. Garzon, R. et al. (2008) Distinctive microRNA signature of acute myeloid leukemia bearing cytoplasmic mutated nucleophosmin. Proc. Natl Acad. Sci. USA, 105, 3945-3950.
22. Garzon, R. et al. (2008) MicroRNA signatures associated with cytogenetics and prognosis in acute myeloid leukemia. Blood, 111, 3183-3189.
23. Gebeshuber, C.A. et al. (2009) miR-29a suppresses tristetraprolin, which is a regulator of epithelial polarity and metastasis. EMBO Rep., 10, 400-405.
24. Gennarino, V.A. et al. (2009) MicroRNA target prediction by expression analysis of host genes. Genome Res., 19, 481-490.
25. Gregory, P.A. et al. (2008) The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nature Cell Biol., 10, 593-601.
26. Griffiths-Jones, S. et al. (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res., 36, D154-D158.
27. He, L. et al. (2007) A microRNA component of the p53 tumour suppressor network. Nature, 447, 1130-1134.
28. Huang da, W. et al. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4, 44-57.
29. Huang, J.C. et al. (2007) Using expression profiling data to identify human microRNA targets. Nature Methods, 4, 1045-1049.
30. Kim, H.K. et al. (2006) Muscle-specific microRNA miR-206 promotes muscle differentiation. J. Cell Biol., 174, 677-687.
31. Korn, E.L. et al. (2007) An investigation of two multivariate permutation methods for controlling the false discovery proportion. Stat. Med., 26, 4428-4440.
32. Krek, A. et al. (2005) Combinatorial microRNA target predictions. Nature Genetics, 37, 495-500.
33. Krutzfeldt, J. et al. (2005) Silencing of microRNAs in vivo with 'antagomirs'. Nature, 438, 685-689.
34. Lagos-Quintana, M. et al. (2001) Identification of novel genes coding for small expressed RNAs. Science, 294, 853-858.
35. Landgraf, P. et al. (2007)Amammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129, 1401-1414.
36. Lau, N.C. et al. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science, 294, 858-862.
37. le Sage, C. et al. (2007) Regulation of the p27(Kip1) tumor suppressor by miR-221 and miR-222 promotes cancer cell proliferation. EMBO J., 26, 3699-3708.
38. Lee, R.C. and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science, 294, 862-864.
39. Lewis, B.P. et al. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20.
40. Maragkakis, M. et al. (2009) DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res., 37, W273-W276.
41. Marcucci, G. et al. (2008) Prognostic significance of, and gene and microRNA expression signatures associated with, CEBPA mutations in cytogenetically normal acute myeloid leukemia with high-risk molecular features: a Cancer and Leukemia Group B Study. J. Clin. Oncol., 26, 5078-5087.
42. Marcucci, G. et al. (2008) MicroRNA expression in cytogenetically normal acute myeloid leukemia. New Engl. J. Med., 358, 1919-1928.
43. Mertens-Talcott, S.U. et al. (2007) The oncogenic microRNA-27a targets genes that regulate specificity protein transcription factors and the G2-M checkpoint in MDAMB-231 breast cancer cells. Cancer Res., 67, 11001-11011.
44. Mott, J.L. et al. (2007) mir-29 regulates Mcl-1 protein expression and apoptosis. Oncogene, 26, 6133-6140.
45. O'Connell, R.M. et al. (2008) Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder. J. Exp. Med., 205, 585-594.
46. Reinhart, B.J. et al. (2000) The 21-nucleotide let-7 RNAregulates developmental timing in Caenorhabditis elegans. Nature, 403, 901-906.
47. Ruby, J.G. et al. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C.elegans. Cell, 127, 1193-1207.
48. Ruby, J.G. et al. (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res., 17, 1850-1864.
49. Selbach, M. et al. (2008) Widespread changes in protein synthesis induced by microRNAs. Nature, 455, 58-63.
50. Simon, R. et al. (2007) Analysis of gene expression data using BRB-array tools. Cancer Inform., 3, 11-17.
51. Sood, P. et al. (2006) Cell-type-specific signatures of microRNAs on target mRNA expression. Proc. Natl Acad. Sci. USA, 103, 2746-2751.
52. Spizzo, R. et al. (2009) SnapShot: MicroRNAs in cancer. Cell, 137, 586-586.e1.
53. Subramanian, A. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
54. Tothova, Z. et al. (2007) FoxOs are critical mediators of hematopoietic stem cell resistance to physiologic oxidative stress. Cell, 128, 325-339.
55. Voorhoeve, P.M. et al. (2006) Agenetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell, 124, 1169-1181.
56. Wilson, K.D. et al. (2009) MicroRNA profiling of human-induced pluripotent stem cells. Stem Cells Dev., 18, 749-758.
57. Wright, G.W. and Simon, R.M. (2003) A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics, 19, 2448-2455.