Combinatorial microRNA target predictions

Nature Genetics

Volumn 37, Issue 5, 2005, Pages 495-500

  Krek, Azra ^a,b   Grün, Dominic ^a   Poy, Matthew N ^c   Wolf, Rachel ^a   Rosenberg, Lauren ^a   Epstein, Eric J ^c   MacMenamin, Philip ^a   Da Piedade, Isabelle ^a   Gunsalus, Kristin C ^a   Stoffel, Markus ^c   Rajewsky, Nikolaus ^a  

^a NEW YORK UNIVERSITY   (United States)

^b POLYTECHNIC UNIVERSITY   (United States)

^c ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

3' UNTRANSLATED REGION; ALGORITHM; ANIMAL CELL; ARTICLE; CELL TYPE; CONTROLLED STUDY; GENE; GENE CONTROL; GENE TARGETING; GENETIC TRANSCRIPTION; GENOME; HUMAN; LET 7B GENE; MATHEMATICAL COMPUTING; MIR 124 GENE; MIR 375 GENE; MOUSE; MTPN GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PICTAR ALGORITHM; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RAT; RNA BINDING; STATISTICAL ANALYSIS; VALIDATION PROCESS; VERTEBRATE;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; MICRORNAS;

EID: 20944450160     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1536     Document Type: Article

References (26)

1. Bartel, D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281-297 (2004).
2. Cullen, B.R. Transcription and processing of human microRNA precursors. Mol. Cell 16, 861-B65 (2004).
3. Ambras, V. The functions of animal microRNAs. Nature 431, 350-355 (2004).
4. Barad, O. et al. MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 14, 2486-2494 (2004).
5. Doench, J.G. & Sharp, P.A. SiRNAs can function as miRNAs. Genes Dev. 17, 438-442 (2003).
6. Hobert, O. Common logic of transcription factor and microRNA action. Trends Biochem. Sci. 29, 426-428 (2004).
7. Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B. & Cohen, S.M. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113, 25-36 (2003).
8. Stark, A., Brennecke, J., Russell, R.B. & Cohen, S.M. Identification of Drosophila microRNA targets. PLoS Biol. 1, E60 (2003).
9. Rajewsky, N. & Socci, N.D. Computational identification of microRNA targets. Dev. Biol. 267, 529-535 (2004).
10. Enright, A.J. et al. MicroRNA targets in Drosophila. Genome Biol. 5, R1 (2003).
11. Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P. & Burge, C.B. Prediction of mammalian microRNA targets. Cell 26, 787-798 (2003).
12. Kiriakidou, M. et al. A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 18, 1165-1178 (2004).
13. John, B. et al. Human MicroRNA targets. PLoS Biol. 2, e363 (2004).
14. Rehmsmeier, M., Steffen, P., Hochsmann, M. & Giegerich, R. Fast and effective prediction of microRNA/target duplexes. RNA 10, 1507-1517 (2004).
15. Rajewsky, N., Vergassola, M., Gaul, U. & Siggia, E.D. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3, 30 (2002).
16. Schroeder, M.D. et al. Transcriptional control in the segmentation gene network of Drosophila. PloS Biol. 2, E271 (2004).
17. Doench, J.G. & Sharp, P.A. Specificity of microRNA target selection in translational repression. Genes Dev. 18, 504-511 (2004).
18. Banerjee, D. & Slack, F. Control of developmental timing by small temporal RNAs: a paradigm for RNA-mediated regulation of gene expression. Bioessays 24, 119-129 (2002).
19. Reinhart, B.J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 24, 901-906 (2000).
20. Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51-54 (2003).
21. Lewis, B.J., Burge, C.B. & Bartel, D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15-20 (2005).
22. Poy, M.N. et al. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226-230 (2004).
23. Pruitt, K.D., Tatusova, T. & Maglott, D. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts, and proteins. Nucleic Acids Res. 33, D501-D504 (2005).
24. International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695-716 (2004).
25. Sinha, S., van Nimwegen, E. & Siggia, E.D. A probabilistic method to detect regulatory modules. Bioinformatics 19, i292-i301 (2003).
26. Griffiths-Jones, S. The microRNA Registry. Nucleic Acids Res. 32, D109-D111 (2004).