Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 34, 2006, Pages 12763-12768

  Biemar, Frédéric ^a   Nix, David A ^b   Piel, Jessica ^a   Peterson, Brant ^a   Ronshaugen, Matthew ^a   Sementchenko, Victor ^b   Bell, Ian ^b   Manak, J Robert ^b   Levine, Michael S ^b  

^a University of California Berkeley   (United States)

^b Thermo Fisher Scientific   (United States)

Author keywords

Gene network; MicroRNA; Noncoding RNA

Indexed keywords

MICRORNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR DORSAL; UNCLASSIFIED DRUG; WNT PROTEIN;

ARTICLE; DROSOPHILA; EMBRYO; EMBRYO DEVELOPMENT; EMBRYO PATTERN FORMATION; ENHANCER REGION; GASTRULATION; GENE CONTROL; GENE IDENTIFICATION; GENOME; INTRON; MORPHOGENESIS; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION;

ANIMALS; BODY PATTERNING; DROSOPHILA MELANOGASTER; EMBRYO, NONMAMMALIAN; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME, INSECT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 33748049810     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0604484103     Document Type: Article

References (45)

1. Moussian, B. & Roth, S. (2005) Curr. Biol. 15, R887-R899.
2. Stathopoulos, A. & Levine, M. (2004) Curr. Opin. Genet. Dev. 14, 477-484.
3. Sokol, N. S. & Ambros, V. (2005) Genes Dev. 19, 2343-2354.
4. Biemar, F., Zinzen, R., Ronshaugen, M., Sementchenko, V., Manak, J. R. & Levine, M. S. (2005) Proc. Natl. Acad. Sci. USA 102, 15907-15911.
5. Kwon, C., Han, Z., Olson, E. N. & Srivastava, D. (2005) Proc. Natl. Acad. Sci. USA 102, 18986-18991.
6. Stathopoulos, A. & Levine, M. (2005) Dev. Cell 9, 449-462.
7. Stathopoulos, A., Van Drenth, M., Erives, A., Markstein, M. & Levine, M. (2002) Cell 111, 687-701.
8. Hino, S., Kishida, S., Michiue, T., Fukui, A., Sakamoto, I., Takada, S., Asashima, M. & Kikuchi, A. (2001) Mol. Cell. Biol. 21, 330-342.
9. Wallingford, J. B. & Habas, R. (2005) Development (Cambridge, U.K.) 132, 4421-4436.
10. Gordon, M. D., Dionne, M. S., Schneider, D. S. & Nusse, R. (2005) Nature 437, 746-749.
11. Ganguly, A., Jiang, J. & Ip, Y. T. (2005) Development (Cambridge, U.K.) 132, 3419-3429.
12. Michiue, T., Fukui, A., Yukita, A., Sakurai, K., Danno, H., Kikuchi, A. & Asashima, M. (2004) Dev. Dyn. 230, 79-90.
13. Treisman, J. E., Lai, Z. C. & Rubin, G. M. (1995) Development (Cambridge, U.K.) 121, 2835-2845.
14. Dobens, L. L., Hsu, T., Twombly, V., Gelbart, W. M., Raftery, L. A. & Kafatos, F. C. (1997) Mech. Dev. 65, 197-208.
15. Law, G. L., Bickel, K. S., MacKay, V. L. & Morris, D. R. (2005) Genome Biol. 6, R111.
16. Brown, C. Y., Mize, G. J., Pineda, M., George, D. L. & Morris, D. R. (1999) Oncogens 18, 5631-5637.
17. Child, S. J., Miller, M. K. & Geballe, A. P. (1999) J. Biol. Chem. 274, 24335-24341.
18. Morris, D. R. & Geballe, A. P. (2000) Mol. Cell. Biol. 20, 8635-8642.
19. O'Connor, M. B., Umulis, D., Othmer, H. G. & Blair, S. S. (2006) Development (Cambridge, U.K.) 133, 183-193.
20. Meller, V. H., Wu, K. H., Roman, G., Kuroda, M. I. & Davis, R. L. (1997) Cell 88, 445-457.
21. Amrein, H. & Axel, R. (1997) Cell 88, 459-469.
22. Tupy, J. L., Bailey, A. M., Dailey, G., Evans-Holm, M., Siebel, C. W., Misra, S., Celniker, S. E. & Rubin, G. M. (2005) Proc. Natl. Acad. Sci. USA 102, 5495-5500.
23. Inagaki, S., Numata, K., Kondo, T., Tomita, M., Yasuda, K., Kanai, A. & Kageyama, Y. (2005) Genes Cells 10, 1163-1173.
24. Aboobaker, A. A., Tomancak, P., Patel, N., Rubin, G. M. & Lai, E. C. (2005) Proc. Natl. Acad. Sci. USA 102, 18017-18022.
25. Cumberledge, S., Zaratzian, A. & Sakonju, S. (1990) Proc. Natl. Acad. Sci. USA 87, 3259-3263.
26. Ronshaugen, M., Biemar, F., Piel, J., Levine, M. & Lai, E. C. (2005) Genes Dev. 19, 2947-2952.
27. Aravin, A. A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J. & Tuschl, T. (2003) Dev. Cell 5, 337-350.
28. Lai, E. C., Tomancak, P., Williams, R. W. & Rubin, G. M. (2003) Genome Biol. 4, R42.
29. Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P. & Gingeras, T. R. (2002) Science 296, 916-919.
30. Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H., et al (2002) Nature 420, 563-573.
31. Kampa, D., Cheng, J., Kapranov, P., Yamanaka, M., Brubaker, S., Cawley, S., Drenkow, J., Piccolboni, A., Bekiranov, S., Helt, G., et al. (2004) Genome Res. 14, 331-342.
32. Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K., Sato, H., Nagai, K., et al. (2004) Nat. Genet. 36, 40-45.
33. Schadt, E. E., Edwards, S. W., GuhaThakurta, D., Holder, D., Ying, L., Svetnik, V., Leonardson, A., Hart, K. W., Russell, A., Li, G., et al. (2004) Genome Biol. 5, R73.
34. Bertone, P., Stolc, V., Royce, T. E., Rozowsky, J. S., Urban, A. E., Zhu, X., Rinn, J. L., Tongprasit, W., Samanta, M., Weissman, S., et al. (2004) Science 306, 2242-2246.
35. Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S., Long, J., Stern, D., Tammana, H., Helt, G., et al. (2005) Science 308, 1149-1154.
36. Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., et al. (2005) Science 309, 1559-1563.
37. Washietl, S., Hofacker, I. L., Lukasser, M., Huttenhofer, A. & Stadler, P. F. (2005) Nat. Biotechnol. 23, 1383-1390.
38. Ravasi, T., Suzuki, H., Pang, K. C., Katayama, S., Furuno, M., Okunishi, R., Fukuda, S., Ru, K., Frith, M. C., Gongora, M. M., et al. (2006) Genome Res. 16, 11-19.
39. Stathopoulos, A., Tam, B., Ronshaugen, M., Frasch, M. & Levine, M. (2004) Genes Dev. 18, 687-699.
40. Yang, Z. (1997) Comput. Appl. Biosci. 13, 555-556.
41. Nekrutenko, A., Makova, K. D. & Li, W.-H. (2002) Genome Res. 12, 198-202.
42. Jiang, J., Kosman, D., Ip, Y. T. & Levine, M. (1991) Genes Dev. 5, 1881-1891.
43. Rebeiz, M. & Posakony, J. W. (2004) Dev. Biol. 271, 431-438.
44. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997) Nucleic Acids Res. 25, 4876-4882.
45. Strimmer, K. & von Haseler, A. (1997) Proc. Natl. Acad. Sci. USA 94, 6815-6819.