REDfly 2.0: An integrated database of cis -regulatory modules and transcription factor binding sites in Drosophila

Nucleic Acids Research

Volumn 36, Issue SUPPL. 1, 2008, Pages

  Halfon, Marc S ^a,b,c   Gallo, Steven M ^b   Bergman, Casey M ^d  

^a UNIVERSITY AT BUFFALO   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

^c ROSWELL PARK CANCER INSTITUTE   (United States)

^d UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; BIOINFORMATICS; DATA ANALYSIS; DROSOPHILA; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE MAPPING; GENETIC DATABASE; GENOMICS; INFORMATION PROCESSING; INFORMATION SERVICE; NONHUMAN; PRIORITY JOURNAL; REDFLY; REGULATORY SEQUENCE; TRANSCRIPTION REGULATION;

ANIMALS; BINDING SITES; DATABASES, GENETIC; DROSOPHILA MELANOGASTER; ENHANCER ELEMENTS (GENETICS); GENOMICS; INTERNET; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SYSTEMS INTEGRATION; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

DROSOPHILA MELANOGASTER; METAZOA;

EID: 38549105493     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm876     Document Type: Article

References (30)

1. Davidson, E.H. (2006) The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, 1st edn. Academic Press, Burlington, MA.
2. Carroll, S.B., Grenier, J.K. and Weatherbee, S.D. (2001) From DNA to Diversity. Molecular Genetics and the Evolution of Animal Design. Blackwell Science, MA.
3. Wray, G.A. (2007) The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet., 8, 206-216.
4. Gallo, S.M., Li, L, Hu, Z. and Halfon, M.S. (2006) REDfly: A Regulatory Element Database for Drosophila. Bioinformatics, 22, 381-383.
5. Bergman, C.M., Carlson, J.W. and Celniker, S.E. (2005) Drosophila DNase I footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics, 21, 1747-1749.
6. Li, L., Zhu, Q., He, X., Sinha, S. and Halfon, M.S. (2007) Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biol., 8, R101.
7. Brody, T., Rasband, W., Baler, K., Kuzin, A., Kundu, M. and Odenwald, W.F. (2007) cis-Decoder discovers constellations of conserved DNA sequences shared among tissue-specific enhancers. Genome Biol., 8, R75.
8. De Renzis, S., Elemento, O, Tavazoie, S. and Wieschaus, E.F. (2007) Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol., 5, e117.
9. Kim, J. and Sinha, S. (2007) Indelign: A probabilistic framework for annotation of insertions and deletions in a multiple alignment. Bioinformatics, 23, 289-297.
10. Sandmann, T., Girardot, C., Brehme, M., Tongprasit, W., Stolc, V. and Furlong, E.E.M. (2007) A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev., 21, 436-449.
11. Sandmann, T., Jensen, L.J., Jakobsen, J.S., Karzynski, M.M., Eichenlaub, M.P., Bork, P. and Furlong, E.E. (2006) A temporal map of transcription factor activity: Mef2 directly regulates target genes at all stages of muscle development. Dev. Cell, 10, 797-807.
12. Macdonald, S.J. and Long, A.D. (2006) Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura. Genome Biol., 7, R67.
13. Papatsenko, D., Kislyuk, A., Levine, M. and Dubchak, I. (2006) Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics, 88, 431-442.
14. Down, T.A., Bergman, C.M., Su, J. and Hubbard, TJ. (2007) Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput. Biol., 3, e7.
15. Dewey, C.N., Huggins, P.M., Woods, K., Sturmfels, B. and Pachter, L. (2006) Parametric alignment of Drosophila genomes. PLoS Comput. Biol. 2, e73.
16. Adryan, B. and Teichmann, S.A. (2006) FlyTF: A systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics, 22, 1532-1533.
17. Glazov, E.A., Pheasant, M., McGraw, E.A., Bejerano, G. and Mattick, J.S. (2005) Ultraconserved elements in insect genomes: A highly conserved intronic Sequence implicated in the control of homothorax mRNA splicing. Genome Res., 15, 800-808.
18. Moses, A.M., Pollard, D.A., Nix, D.A., Iyer, V.N., Li, X.-Y., Biggin, M.D. and Eisen, M.B. (2006) Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comp. Biol. 2, e130.
19. Pierstorff, N., Bergman, C.M. and Wiehe, T. (2006) Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics, 22, 2858-2864.
20. Pollard, D.A., Moses, A.M., Iyer, V.N. and Eisen, M.B. (2006) Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics, 7 376.
21. Crosby, M.A., Goodman, J.L., Strelets, V.B., Zhang, P. and Gelbart, W.M. (2007) FlyBase: Genomes by the dozen. Nucleic Acids Res., 35 D486-D491.
22. Lyne, R., Smith, R., Rutherford, K, Wakeling, M., Varley, A., Guillier, F., Janssens, H., Ji, W., McLaren, P. et al. (2007) Fly Mine: Ah integrated database for Drosophila and Anopheles genomics. Genome Biol., 8, R129.
23. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M. and Haussler, D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
24. Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W. et al. (2002) The generic genome browser: A building block for a model organism system database. Genome Res., 12, 1599-1610.
25. Drysdale, R. (2001) Phenotypic data in FlyBase: Brief Bioinform., 2, 68-80.
26. Tomancak, P., Berman, B.P., Beaton, A., Weiszmann, R., Kwan, E., Hartenstein, V., Celniker, S.E. and Rubin, G.M. (2007) Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol., 8, R145.
27. Tomancak, P., Beaton, A., Weiszmann, R., Kwan, E., Shu, S, Lewis, S.E., Richards, S., Ashburner, M., Hartenstein, V. et al. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol., 3, RESEARCH0088.
28. Montgomery, S.B., Griffith, O.L., Sleumer, M.C., Bergman, C.M., Bilenky, M., Pleasance, E.D., Prychyna, Y., Zhang, X. and Jones, S.J.M. (2006) ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics, 22, 637-640.
29. Van Emden, B., Ramos, H, Panchanathan, S., Newfeld, S.J. and Kumar, S. (2006) FlyExpress: An image-matching web-tool for finding genes with overlapping patterns of expression in Drosophila embryos. Arizona State University, Tempe, AZ, www.flyexpress.net.
30. Eilbeck, K., Lewis, S.E., Mungall, C.J., Yandell, M., Stein, L., Durbin, R. and Ashburner, M. (2005) The Sequence Ontology: A tool for the unification of genome annotations. Genome Biol., 6, R44.