Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

BMC Bioinformatics

Volumn 3, Issue , 2002, Pages

  Rajewsky, Nikolaus ^a   Vergassola, Massimo ^a,b   Gaul, Ulrike ^a   Siggia, Eric D ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b UNIVERSITÉ CÔTE D'AZUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; TRANSCRIPTION FACTOR;

ACCURACY; ANIMAL CELL; ARTICLE; BINDING SITE; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONTROLLED STUDY; DROSOPHILA; EMBRYO PATTERN FORMATION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC CODE; GENETIC REGULATION; INTERNET; MATHEMATICAL COMPUTING; MORPHOGENESIS; NONHUMAN; PREDICTION; PROTEIN MOTIF; SCORING SYSTEM; STATISTICAL ANALYSIS; TRANSCRIPTION REGULATION;

EID: 2942576308     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-3-30     Document Type: Article

References (19)

1. Rubin GM, Yandell MD, et al: Comparative Genomics of the Eukaryotes. Science 2000, 287:2204-15
2. Brivanlou AH, Darnell JE Jr: Signal transduction and the control of gene expression. Science 2002, 295:813-8
3. Davidson EH: Genomic regulatory systems. Academic Press, San Diego 2001
4. Davidson EH, Rast JP, et al: A genomic regulatory network for development. Science 2002, 295:1669-78
5. Arnone MI, Davidson EH: The hardwiring of development: organization and function of genomic regulatory systems. Development 1997, 124:1851-64
6. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB: Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci USA 2002, 99:757-762
7. Markstein M, Markstein P, Markstein V, Levine MS: Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci USA 2002, 99:763-768
8. Halfon MS, Grad Y, Church GM, Michelson AM: Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res 2002, 12:1019-28
9. Papatsenko DA, Makeev VJ, Lifanov AP, Regnier M, Nazina AG, Desplans C: Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. Genome Res 2002, 12:470-81
10. Wieschaus E: Embryonic transcription and the control of developmental pathways. Genetics 1996, 142:5-10
11. Bussemaker HJ, Li H, Siggia ED: Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc Natl Acad Sci USA 2000, 97:10096-100
12. Jiang J, Levine M: Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen. Cell 1993, 72:741-52
13. Ryoo HD, Marty T, Casares F, Affolter M, Mann RS: Regulation of Hox target genes by a DNA bound Homothorax/Hox/Extradenticle complex. Development 1999, 126:5137-48
14. Courey AJ, Jia S: Genes and Development Transcriptional repression: the long and the short of it. Genes and Development 2001, 15:2786-96
15. Zhang M, Siggia ED, Li H: private communication.
16. van Nimwegen E, Zavolan M, Rajewsky N, Siggia ED: Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proc Natl Acad Sci USA 2002, 99:7323-7328
17. Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999, 27:573-80
18. Hertz GZ, Hartzell III GW, Stormo GD: Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci 1990, 6:81-92
19. Abril JF, Guigo R: gff2ps: visualizing genomic annotations. Bioinformatics 2000, 16:743-744