Abstract
How each microRNA regulates gene expression is unknown problem. Especially, which gene is targeted by each microRNA is mainly depicted via computational method, typically without biological/ experimental validations. In this paper, we propose a new computational method, MiRaGE, to detect gene expression regulation via miRNAs by the use of expression profile data and miRNA target prediction. This method is tested to miRNA transfection experiments to tumor cells and succeeded in inference of transfected miRNA as only one miRNA with significant P-values for the first time.
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Brennecke, J., Stark, A., Russell, R.B., Cohen, S.M.: Principles of MicroRNA-targetRecognition. PLoS Biol. 3, 85 (2005)
Chi, S.W., Zang, J.B., Mele, A., Darnell, R.B.: Argonaute HITS-CLIP Decodes MicroRNA-mRNA Interaction Maps. Nature 460(7254), 479–486 (2009)
Takahashi, Y., Forrest, A.A.R., Maeno, E., Hashimoto, T., Daub, C.O., Yasuda, J.: MiR-107 and MiR-185 Can Induce Cell cycle Arrest in Human Non Small Cell Lung Cancer Cell Lines? PLoS One 4, e6677 (2009)
Ikeo, K., Ishii, J., Tamura, T., Gojobori, T., Tateno, Y.: CIBEX: center for information biology gene expression database. C R Biol. 326, 1079–1082 (2003)
Nielsen, C.B., Shomron, N., Sandberg, R., Hornstein, E., Kitzman, J., Burge, C.B.: Determinants of Targeting by Endogenous and Exogenous MicroRNAs and siRNAs. RNA 13, 1894–1910 (2007)
Friedman, R.C., Farh, K.K., Burge, C.B., Bartel, D.P.: Most Mammalian mRNAs are Conserved Targets of MicroRNAs. Genome Res. 19, 92–105 (2009)
Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., Segal, E.: The Role of Site Accessibility in MicroRNA Target Recognition. Nat. Genet. 39, 1278–1284 (2007)
Krek, A., Grün, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., da Piedade, I., Gunsalus, K.C., Stoffel, M., Rajewsky, N.: Combinatorial MicroRNA Target Predictions. Nat. Genet. 37, 495–500 (2005)
John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., Marks, D.S.: Human MicroRNA Targets. PLoS Biol. 2, e363 (2004)
Alexiou, P., Maragkakis, M., Papadopoulos, G.L., Reczko, M., Hatzigeorgiou, A.G.: Lost in Translation: An Assessment and Perspective for Computational MicroRNA Target Identification. Bioinformatics 25, 3049–3055 (2009)
Taguchi, Y.-h., Yasuda, J.: Inference of gene expression regulation via microRNA transfection. In: Huang, D.-S., Zhao, Z., Bevilacqua, V., Figueroa, J.C. (eds.) ICIC 2010. LNCS, vol. 6215, pp. 672–679. Springer, Heidelberg (2010)
Benjamini, Y., Hochberg, Y.: Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J. R. Stat. Soc. B 57, 289–300 (1995)
R Development Core Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2009) ISBN 3-900051-07-0, http://www.R-project.org
Volinia, S., Visone, R., Galasso, M., Rossi, E., Croce, C.: Identification of MicroRNA Activity by Targets’ Reverse EXpression. Bioinformatics 26, 91–97 (2010)
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Taguchi, Yh., Yasuda, J. (2012). MiRaGE: Inference of Gene Expression Regulation via MicroRNA Transfection II. In: Huang, DS., Gan, Y., Premaratne, P., Han, K. (eds) Bio-Inspired Computing and Applications. ICIC 2011. Lecture Notes in Computer Science(), vol 6840. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24553-4_19
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DOI: https://doi.org/10.1007/978-3-642-24553-4_19
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