Prediction of Targets for MicroRNAs

Methods in Molecular Biology

Volumn 703, Issue , 2011, Pages 311-317

  Lindow, Morten ^a  

^a Santaris Pharma AS   (Denmark)

Author keywords

MicroRNA; post transcriptional regulation; RNA RNA interaction; target prediction

Indexed keywords

MESSENGER RNA; MICRORNA;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; INTERNET; METABOLISM; METHODOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION REGULATION; INTERNET; MICRORNAS; RNA, MESSENGER; SOFTWARE;

MLCS; MLOWN;

EID: 79952607868     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-59745-248-9_21     Document Type: Chapter

References (20)

1. Bentwich, I. (2005) Prediction and validation of microRNAs and their targets. FEBS Lett 579, 5904–5910.
2. Lindow, M., Gorodkin, J. (2007) Principles and limitations of computational miRNA gene and target finding. Cell DNA Biol. May, 26(5):339–51.
3. Yoon, S., De Micheli, G. (2006) Computational identification of microRNAs and their targets. Birth Defects Res C Embryo Today 78, 118–128.
4. Rhoades, M. W., Reinhart, B. J., Lim, L. P., Burge, C. B., Bartel, B., Bartel, D. P. (2002) Prediction of plant microRNA targets. Cell 110, 513–520.
5. Chen, X. (2005) MicroRNA biogenesis and function in plants. FEBS Lett 579, 5923– 5931.
6. ′ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30, 363–364.
7. Brennecke, J., Stark, A., Russell, R. B., Cohen, S. M. (2005) Principles of microRNA-target recognition. PLoS Biol 3, e85.
8. Lewis, B. P., Burge, C. B., Bartel, D. P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20.
9. ′ UTR evolution. Cell 123, 1133–1146.
10. Didiano, D., Hobert, O. (2006) Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions. Nat Struct Mol Biol 13, 849–851.
11. Lim, L. P., Lau, N. C., Garrett-Engele, P., Grimson, A., Schelter, J. M., Castle, J., Bartel, D. P., Linsley, P. S., Johnson, J. M. (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769–773.
12. Krutzfeldt, J., Rajewsky, N., Braich, R., Rajeev, K. G., Tuschl, T., Manoharan, M., Stoffel, M. (2005) Silencing of microRNAs in vivo with ‘antagomirs’. Nature 438, 685– 689.
13. Vinther, J., Hedegaard, M. M., Gardner, P. P., Andersen, J. S., Arctander, P. (2006) Identification of miRNA targets with stable isotope labeling by amino acids in cell culture. Nucleic Acids Res 34, e107.
14. Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C., Marks, D. S. (2003) MicroRNA targets in Drosophila. Genome Biol 5, R1.
15. John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., Marks, D. S. (2004) Human MicroRNA targets. PLoS Biol 2, e363.
16. Grun, D., Wang, Y. L., Langenberger, D., Gunsalus, K. C., Rajewsky, N. (2005) microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol 1, e13.
17. Krek, A., Grun, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., MacMenamin, P., da Piedade, I., Gunsalus, K. C., Stoffel, M., Rajewsky, N. (2005) Combinatorial microRNA target predictions. Nat Genet 37, 495–500.
18. Lall, S., Grun, D., Krek, A., Chen, K., Wang, Y. L., Dewey, C. N., Sood, P., Colombo, T., Bray, N., Macmenamin, P., Kao, H. L., Gunsalus, K. C., Pachter, L., Piano, F., Rajewsky, N. (2006) A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol 16, 460–471.
19. Rehmsmeier, M., Steffen, P., Hochsmann, M., Giegerich, R. (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507–1517.
20. Karlin, S., Altschul, S. F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci USA 87, 2264–2268.