TarBase: A comprehensive database of experimentally supported animal microRNA targets

RNA

Volumn 12, Issue 2, 2006, Pages 192-197

  Sethupathy, Praveen ^a   Corda, Benoit ^a   Hatzigeorgiou, Artemis G ^a,b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Computational; Database; Experimentally supported; microRNA; microRNA target

Indexed keywords

MICRORNA;

ARTICLE; DATA BASE; DATA EXTRACTION; DROSOPHILA; GENE REPRESSION; PREDICTION; PRIORITY JOURNAL; RNA BINDING; RNA CLEAVAGE; RNA TRANSLATION; WORM; ZEBRA FISH;

3' UNTRANSLATED REGIONS; ANIMALS; DATABASES, GENETIC; GENE EXPRESSION REGULATION; MICRORNAS; USER-COMPUTER INTERFACE;

ANIMALIA; DANIO RERIO; DROSOPHILA MELANOGASTER; MAMMALIA;

EID: 31044444975     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2239606     Document Type: Article

References (49)

1. Abrahante, J.E., Daul, A.L., Li, M., Volk, M.L., Tennessen, J.M., Miller, E.A., and Rougvie, A.E. 2003. The Caenorhabditis elegans hunchback-like GENE lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev. Cell 4: 625-637.
2. Bartel, D.P. 2004. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
3. Bentwich, I., Avniel, A., Karov, Y., Aharonov, R., Gilad, S., Barad, O., Barzilai, A., Einat, P., Finav, U., Meiri, E., et al. 2005. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37: 766-770.
4. Berezikov, E., Guryev, V., van de Belt, J., Wienholds, E., Plasterk, R.H., and Cuppen, E. 2005. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120: 21-24.
5. Brennecke, J., Hipfner, D.R., Stark, A., Russell, R.B., and Cohen, S.M. 2003. bantam encodes a developmentally regulated microRNA that controls cells proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113: 25-36.
6. Brennecke, J., Stark, A., Russell, R.B., and Cohen, S.M. 2005. Principles of microRNA-target recognition. PLoS Biol. 3: 404-418.
7. Burgler, C. and Macdonald, P.M. 2005. Prediction and verification of microRNA targets by MovingTargets, a highly adaptable prediction method. BMC Genomics 6: 88.
8. Chang, S., Johnston, R.J., Frakjaer-Jensen, C., Lockery, S., and Hobert, O. 2004. MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430: 785-789.
9. Cimmino, A., Calin, G.A., Fabbri, M., Iorio, M.V., Ferracin, M., Shimizu, M., Wojcik, S.E., Aqeilan, R.I., Zupo, S., Dono, M., et al. 2005. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc. Natl. Acad. Sci. 102: 13944-13949.
10. Davis, E., Caiment, F., Tordoir, X., Cavaille, J., Ferguson-Smith, A., Cockett, N., Georges, M., and Charlier, C. 2005. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. Curr. Biol. 15: 743-749.
11. Enright, A.J., John, B., Gaul, U., Tuschl, T., Sander, C., and Marks, D.S. 2003. MicroRNA targets in Drosophila. Genome Biol. 5: R1.
12. Esau, C., Kang, X., Peralta, E., Hanson, E., Marcusson, E.G., Ravichandran, L.V., Sun, Y., Koo, S., Perera, R.J., Jain, R., et al. 2004. MicroRNA-143 regulates adipocyte differentiation. J. Biol. Chem. 279: 52361-52365.
13. Grosshans, H., Johnson, T., Reinert, K.L., Gerstein, M., and Slack, F.J. 2005. The temporal patterning microRNA let-7 regulates several transcription factors at the larval to adult transition in C. elegans. Dev. Cell 8: 321-330.
14. Grun, D., Wang, Y., Langenberger, D., Gunsalus, K.C., and Rajewsky, N. 2005. microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput. Biol. 1: 51-66.
15. John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., and Marks, D.S. 2004. Human microRNA targets. PLoS Biol. 2: 1862-1879.
16. Johnson, S.M., Grosshans, H., Shingara, J., Byrom, M., Jarvis, R., Cheng, A., Labourier, E., Reinert, K.L., Brown, D., and Slack, F.J. 2005. RAS is regulated by the let-7 microRNA family. Cell 120: 635-647.
17. Johnston, R.J. and Hobert, O. 2003. A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature 426: 845-849.
18. Kawasaki, H. and Taira, K. 2005. Identification of target genes of microRNAs in retinoic acid-induced neuronal differentiation. Pure Appl. Chem. 77: 313-318.
19. Kiriakidou, M., Nelson, P., Kouranov, A., Fitziev, P., Bouyioukos, C., Mourelatos, Z., and Hatzigeorgiou, A.G. 2004. A combined computational- experimental approach predicts human miRNA targets. Genes & Dev. 18: 1165-1178.
20. Kloosterman, W.P., Wienholds, E., Ketting, R.F., and Plasterk, R.H.A. 2004. Substrate requirements for let-7 function in the developing zebrafish embryo. Nucleic Acids Res. 32: 6284-6291.
21. Krek, A., Grun, D., Poy, M.N., Wolf, R., Rosenberg, L., Epstein, E.J., MacMenamin, P., Piedade, I., Gunsalus, K.C., Stoffel, M., et al. 2005. Combinatorial microRNA target predictions. Nat. Genet. 37: 495-500.
22. Lai, E.C., Tam, B., and Rubin, G.M. 2005. Pervasive regulation of Drosophila Notch target genes by GY-box-, Brd-box-, and K-box-class microRNAs. Genes & Dev. 19: 1067-1080.
23. Leaman, D., Chen, P.Y., Fak, J., Yalcin, A., Pearce, M., Unnerstall, U., Marks, D.S., Sander, C., Tuschl, T., and Gaul, U. 2005. Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell 121: 1097-1108.
24. Lecellier, C., Dunoyer, P., Arar, K., Lehmann-Che, J., Eyquem, S., Himber, C., Saib, A., and Voinnet, O. 2005. A cellular micro-RNA mediates antiviral defense in human cells. Science 308: 557-560.
25. Lee, R.C., Feinbaum, R.L., and Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843-854.
26. Lewis, B.P., Shih, I., Jones-Rhoades, M.W., Bartel, D.P., and Burge, C.B. 2003. Prediction of mammalian microRNA targets. Cell 115: 787-798.
27. Lewis, B.P., Burge, C.B., and Bartel, D.P. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120: 15-20.
28. Lim, L.P., Glasner, M.E., Yekta, S., Burge, C.B., and Bartel, D.P. 2003. Vertebrate microRNA genes. Science 299: 5612.
29. Lim, L.P., Lau, N.C., Garrett-Engele, P., Grimson, A., Schelter, J.M., Castle, J., Bartel, D.P., Linsley, P.S., and Johnson, J.M. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433: 769-773.
30. Lin, S.Y., Johnson, S.M., Abraham, M., Vella, M.C., Pasquinelli, A., Gamberi, C., Gottlieb, E., and Slack, F.J. 2003. The C. elegans hunchback homolog, hbl-1, controls temporal patterning and is a probable microRNA target. Dev. Cell 4: 639-650.
31. Moss, E.G., Lee, R.C., and Ambros, V. 1997. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88: 637-646.
32. Nakamoto, M., Jin, P., O'Donnell, W.T., and Warren, S.T. 2005. Physiological identification of human transcripts translationally regulated by a specific microRNA. Hum. Mol. Genet. http://hmg.oxfordjournals.org/cgi/content/ abstract/ddi397v1
33. O'Donnell, K.A., Wentzel, E.A., Zeller, K.I., Dang, C.V., and Mendell, J.T. 2005. c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435: 839-843.
34. Pillai, R.S., Bhattacharyya, S.N., Artus, C.G., Zoller, T., Cougot, N., Basyuk, E., Bertrand, E., and Filipowicz, W. 2005. Inhibition of translational initiation by Let-7 microRNA in human cells. Science 309: 573-576.
35. Poy, M.N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma., X., MacDonald, P.E., Pfeffer, S., Tuschl, T., Rajewsky, N., Rorsman, P., et al. 2004. A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432: 226-230.
36. Rajewsky, N. and Socci, N.D. 2004. Computational identification of microRNA targets. Dev. Biol. 267: 529-535.
37. Rehmsmeier, M., Steffen, P., Hochsmann, M., and Giegerich, R. 2004. Fast and effective prediction of microRNA/target duplexes. RNA 10: 1507-1517.
38. Reinhart, B.J., Slack, F.J., Basson, M., Pasquinelli, A.E., Bettinger, J.C., Rougvie, A.E., Horvitz, H.R., and Ruvkun, G. 2000. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403: 901-905.
39. Robins, H., Li, Y., and Padgett, R.W. 2005. Incorporating structure to predict microRNA targets. Proc. Natl. Acad. Sci. 102: 4006-4009.
40. Rusinov, V., Baev, V., Minkov, I.N., and Tabler, M. 2005. Micro-Inspector: A Web tool for detection of miRNA binding sites in an RNA sequence. Nucleic Acids Res. 33: 696-700.
41. Saetrom, O., Snove Jr., O., and Saetrom, P. 2005. Weighted sequence motifs as an improved seeding step in microRNA target prediction algorithms. RNA 11: 995-1003.
42. Slack, F.J., Basson, M., Liu, Z., Ambros, V., Horvitz, H.R., and Ruvkun, G. 2000. The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Mol. Cell 5: 659-669.
43. Stark, A., Brennecke, J., Russell, R.B., and Cohen, S.M. 2003. Identification of Drosophila microRNA targets. PLoS Biol. 1: 1-13.
44. Wightman, B., Ha, I., and Ruvkun, G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855-862.
45. Wu, L. and Belasco, J.G. 2005. Micro-RNA regulation of the mammalian lin-28 gene during neuronal differentiation of the embryonal carcinoma cells. Mol. Cell. Biol. 25: 9198-9208.
46. Xie, X., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S., and Kellis, M. 2005. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434: 338-345.
47. Xu, P., Vernooy, S.Y., Guo, M., and Hay, B.A. 2003. The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 13: 790-795.
48. Yekta, S., Shih, I., and Bartel, D.P. 2004. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304: 594-596.
49. Zhao, Y., Samal, E., and Srivastava, D. 2005. Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature 436: 214-220.