메뉴 건너뛰기




Volumn 350, Issue 2, 2011, Pages 239-254

When needles look like hay: How to find tissue-specific enhancers in model organism genomes

Author keywords

Cis regulation; Cis regulatory element; Enhancers; Fish; Genome analysis; Medaka; Non coding elements; Transcriptional regulation; Transgenesis; Zebrafish

Indexed keywords

BETA GLOBIN;

EID: 79151469568     PISSN: 00121606     EISSN: 1095564X     Source Type: Journal    
DOI: 10.1016/j.ydbio.2010.11.026     Document Type: Review
Times cited : (24)

References (298)
  • 1
    • 39749093935 scopus 로고    scopus 로고
    • Genomic mapping of suppressor of hairy-wing binding sites in Drosophila
    • Adryan B., Woerfel G., Birch-Machin I., et al. Genomic mapping of suppressor of hairy-wing binding sites in Drosophila. Genome Biol. 2007, 8:R167.
    • (2007) Genome Biol. , vol.8
    • Adryan, B.1    Woerfel, G.2    Birch-Machin, I.3
  • 2
    • 36448971223 scopus 로고    scopus 로고
    • In vivo characterization of human Apoa5 haplotypes
    • Ahituv N., Akiyama J., Chapman-Helleboid A., et al. In vivo characterization of human Apoa5 haplotypes. Genomics 2007, 90:674-679.
    • (2007) Genomics , vol.90 , pp. 674-679
    • Ahituv, N.1    Akiyama, J.2    Chapman-Helleboid, A.3
  • 3
    • 27544443178 scopus 로고    scopus 로고
    • Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny
    • Ahituv N., Prabhakar S., Poulin F., et al. Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. Hum. Mol. Genet. 2005, 14:3057-3063.
    • (2005) Hum. Mol. Genet. , vol.14 , pp. 3057-3063
    • Ahituv, N.1    Prabhakar, S.2    Poulin, F.3
  • 4
    • 34548697503 scopus 로고    scopus 로고
    • Deletion of ultraconserved elements yields viable mice
    • Ahituv N., Zhu Y., Visel A., et al. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 2007, 5:e234.
    • (2007) PLoS Biol. , vol.5
    • Ahituv, N.1    Zhu, Y.2    Visel, A.3
  • 5
    • 33745685239 scopus 로고    scopus 로고
    • Unraveling cis-regulatory mechanisms at the abdominal-a and abdominal-b genes in the drosophila bithorax complex
    • Akbari O.S., Bousum A., Bae E., et al. Unraveling cis-regulatory mechanisms at the abdominal-a and abdominal-b genes in the drosophila bithorax complex. Dev. Biol. 2006, 293:294-304.
    • (2006) Dev. Biol. , vol.293 , pp. 294-304
    • Akbari, O.S.1    Bousum, A.2    Bae, E.3
  • 6
    • 56949091456 scopus 로고    scopus 로고
    • Noncoding RNA in development
    • Amaral P.P, Mattick J.S. Noncoding RNA in development. Mamm. Genome 2008, 19:454-492.
    • (2008) Mamm. Genome , vol.19 , pp. 454-492
    • Amaral, P.P.1    Mattick, J.S.2
  • 7
    • 0028962333 scopus 로고
    • Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes
    • Aparicio S., Morrison A., Gould A., et al. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl. Acad. Sci. U.S.A. 1995, 92:1684-1688.
    • (1995) Proc. Natl. Acad. Sci. U.S.A. , vol.92 , pp. 1684-1688
    • Aparicio, S.1    Morrison, A.2    Gould, A.3
  • 8
    • 21344466736 scopus 로고    scopus 로고
    • The tissue-specific methylation of the human tyrosine hydroxylase gene reveals new regulatory elements in the first exon
    • Arányi T., Faucheux B.A., Khalfallah O., et al. The tissue-specific methylation of the human tyrosine hydroxylase gene reveals new regulatory elements in the first exon. J. Neurochem. 2005, 94:129-139.
    • (2005) J. Neurochem. , vol.94 , pp. 129-139
    • Arányi, T.1    Faucheux, B.A.2    Khalfallah, O.3
  • 9
    • 38349004477 scopus 로고    scopus 로고
    • Developmental biology and databases: how to archive, find and query gene expression patterns using the world wide web
    • Armit C. Developmental biology and databases: how to archive, find and query gene expression patterns using the world wide web. Organogenesis 2007, 3:70-73.
    • (2007) Organogenesis , vol.3 , pp. 70-73
    • Armit, C.1
  • 10
    • 0030986188 scopus 로고    scopus 로고
    • The hardwiring of development: organization and function of genomic regulatory systems
    • Arnone M.I., Davidson E.H. The hardwiring of development: organization and function of genomic regulatory systems. Development (Cambridge, England) 1997, 124:1851-1864.
    • (1997) Development (Cambridge, England) , vol.124 , pp. 1851-1864
    • Arnone, M.I.1    Davidson, E.H.2
  • 11
    • 0037209074 scopus 로고    scopus 로고
    • Analysis and function of transcriptional regulatory elements: insights from Drosophila
    • Arnosti D.N. Analysis and function of transcriptional regulatory elements: insights from Drosophila. Annu. Rev. Entomol. 2003, 48:579-602.
    • (2003) Annu. Rev. Entomol. , vol.48 , pp. 579-602
    • Arnosti, D.N.1
  • 12
    • 58149302266 scopus 로고    scopus 로고
    • Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells
    • Attanasio C., Reymond A., Humbert R., et al. Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biol. 2008, 9:R168.
    • (2008) Genome Biol. , vol.9
    • Attanasio, C.1    Reymond, A.2    Humbert, R.3
  • 14
    • 0019811465 scopus 로고
    • Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences
    • Banerji J., Rusconi S., Schaffner W. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell 1981, 27:299-308.
    • (1981) Cell , vol.27 , pp. 299-308
    • Banerji, J.1    Rusconi, S.2    Schaffner, W.3
  • 15
    • 48249144806 scopus 로고    scopus 로고
    • A transcriptional enhancer from the coding region of Adamts5
    • Barthel K.K.B., Liu X. A transcriptional enhancer from the coding region of Adamts5. PLoS ONE 2008, 3:e2184.
    • (2008) PLoS ONE , vol.3
    • Barthel, K.K.B.1    Liu, X.2
  • 16
    • 0035810946 scopus 로고    scopus 로고
    • Regulation of the stem cell leukemia (PAX) gene: a tale of two fishes
    • Barton L.M., Gottgens B., Gering M., et al. Regulation of the stem cell leukemia (PAX) gene: a tale of two fishes. Proc. Natl. Acad. Sci. USA 2001, 98:6747-6752.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 6747-6752
    • Barton, L.M.1    Gottgens, B.2    Gering, M.3
  • 17
    • 33646928347 scopus 로고    scopus 로고
    • A distal enhancer and an ultraconserved exon are derived from a novel retroposon
    • Bejerano G., Lowe C.B., Ahituv N., et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 2006, 441:87-90.
    • (2006) Nature , vol.441 , pp. 87-90
    • Bejerano, G.1    Lowe, C.B.2    Ahituv, N.3
  • 18
    • 2542542256 scopus 로고    scopus 로고
    • Ultraconserved elements in the human genome
    • Bejerano G., Pheasant M., Makunin I., et al. Ultraconserved elements in the human genome. Science 2004, 304:1321-1325.
    • (2004) Science , vol.304 , pp. 1321-1325
    • Bejerano, G.1    Pheasant, M.2    Makunin, I.3
  • 19
    • 0034883255 scopus 로고    scopus 로고
    • Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences
    • Bergman C.M., Kreitman M. Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res. 2001, 11:1335-1345.
    • (2001) Genome Res. , vol.11 , pp. 1335-1345
    • Bergman, C.M.1    Kreitman, M.2
  • 20
    • 0037154273 scopus 로고    scopus 로고
    • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    • Berman B.P., Nibu Y., Pfeiffer B.D., et al. 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.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 757-762
    • Berman, B.P.1    Nibu, Y.2    Pfeiffer, B.D.3
  • 21
    • 12744263842 scopus 로고    scopus 로고
    • Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
    • Berman B.P., Pfeiffer B.D., Laverty T.R., et al. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 2004, 5:R61.
    • (2004) Genome Biol. , vol.5
    • Berman, B.P.1    Pfeiffer, B.D.2    Laverty, T.R.3
  • 23
    • 33746219660 scopus 로고    scopus 로고
    • The design of transcription-factor binding sites is affected by combinatorial regulation
    • Bilu Y., Barkai N. The design of transcription-factor binding sites is affected by combinatorial regulation. Genome Biol. 2005, 6:R103.
    • (2005) Genome Biol. , vol.6
    • Bilu, Y.1    Barkai, N.2
  • 24
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the encode pilot project
    • Birney E., Stamatoyannopoulos J.A., Dutta A., et al. Identification and analysis of functional elements in 1% of the human genome by the encode pilot project. Nature 2007, 447:799-816.
    • (2007) Nature , vol.447 , pp. 799-816
    • Birney, E.1    Stamatoyannopoulos, J.A.2    Dutta, A.3
  • 25
    • 33745152719 scopus 로고    scopus 로고
    • Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression
    • Blanchette M., Bataille A.R., Chen X., et al. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res. 2006, 16:656-668.
    • (2006) Genome Res. , vol.16 , pp. 656-668
    • Blanchette, M.1    Bataille, A.R.2    Chen, X.3
  • 26
    • 77956641239 scopus 로고    scopus 로고
    • Chip-seq identification of weakly conserved heart enhancers
    • Blow M.J., McCulley D.J., Li Z., et al. Chip-seq identification of weakly conserved heart enhancers. Nat. Genet. 2010, 42:806-810.
    • (2010) Nat. Genet. , vol.42 , pp. 806-810
    • Blow, M.J.1    McCulley, D.J.2    Li, Z.3
  • 28
    • 21244491189 scopus 로고    scopus 로고
    • Identification of Pax2-regulated genes by expression profiling of the mid-hindbrain organizer region
    • Bouchard M., Grote D., Craven S.E., et al. Identification of Pax2-regulated genes by expression profiling of the mid-hindbrain organizer region. Development 2005, 132:2633-2643.
    • (2005) Development , vol.132 , pp. 2633-2643
    • Bouchard, M.1    Grote, D.2    Craven, S.E.3
  • 30
    • 66449114042 scopus 로고    scopus 로고
    • Functional diversity for rest (nrsf) is defined by in vivo binding affinity hierarchies at the DNA sequence level
    • Bruce A.W., López-Contreras A.J., Flicek P., et al. Functional diversity for rest (nrsf) is defined by in vivo binding affinity hierarchies at the DNA sequence level. Genome Res. 2009.
    • (2009) Genome Res.
    • Bruce, A.W.1    López-Contreras, A.J.2    Flicek, P.3
  • 31
    • 0035477093 scopus 로고    scopus 로고
    • Enhancer-promoter specificity mediated by dpe or tata core promoter motifs
    • Butler J.E., Kadonaga J.T. Enhancer-promoter specificity mediated by dpe or tata core promoter motifs. Genes Dev. 2001, 15:2515-2519.
    • (2001) Genes Dev. , vol.15 , pp. 2515-2519
    • Butler, J.E.1    Kadonaga, J.T.2
  • 32
    • 23844495172 scopus 로고    scopus 로고
    • An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules
    • Cameron R.A., Chow S.H., Berney K., et al. An evolutionary constraint: strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules. Proc. Natl. Acad. Sci. USA 2005, 102:11769-11774.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 11769-11774
    • Cameron, R.A.1    Chow, S.H.2    Berney, K.3
  • 33
    • 0842301371 scopus 로고    scopus 로고
    • Cis-regulatory activity of randomly chosen genomic fragments from the sea urchin
    • Cameron R.A., Oliveri P., Wyllie J., et al. Cis-regulatory activity of randomly chosen genomic fragments from the sea urchin. Gene Expr. Patterns 2004, 4:205-213.
    • (2004) Gene Expr. Patterns , vol.4 , pp. 205-213
    • Cameron, R.A.1    Oliveri, P.2    Wyllie, J.3
  • 34
    • 0036898580 scopus 로고    scopus 로고
    • Long-range chromatin regulatory interactions in vivo
    • Carter D., Chakalova L., Osborne C.S., et al. Long-range chromatin regulatory interactions in vivo. Nat. Genet. 2002, 32:623-626.
    • (2002) Nat. Genet. , vol.32 , pp. 623-626
    • Carter, D.1    Chakalova, L.2    Osborne, C.S.3
  • 35
    • 35348873167 scopus 로고    scopus 로고
    • Purifying selection maintains highly conserved noncoding sequences in Drosophila
    • Casillas S., Barbadilla A., Bergman C.M. Purifying selection maintains highly conserved noncoding sequences in Drosophila. Mol. Biol. Evol. 2007, 24:2222-2234.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 2222-2234
    • Casillas, S.1    Barbadilla, A.2    Bergman, C.M.3
  • 36
    • 58149279450 scopus 로고    scopus 로고
    • RNA profiling of FAC-sorted neurons from the developing zebrafish spinal cord
    • Cerda G.A., Hargrave M., Lewis K.E. RNA profiling of FAC-sorted neurons from the developing zebrafish spinal cord. Dev. Dyn. 2009, 238:150-161.
    • (2009) Dev. Dyn. , vol.238 , pp. 150-161
    • Cerda, G.A.1    Hargrave, M.2    Lewis, K.E.3
  • 37
    • 34248213721 scopus 로고    scopus 로고
    • Detecting non-coding selective pressure in coding regions
    • Chen H., Blanchette M. Detecting non-coding selective pressure in coding regions. BMC Evol. Biol. 2007, 7(Suppl 1):S9.
    • (2007) BMC Evol. Biol. , vol.7 , Issue.SUPPL 1
    • Chen, H.1    Blanchette, M.2
  • 38
    • 0037133627 scopus 로고    scopus 로고
    • Enhancer action in trans is permitted throughout the Drosophila genome
    • Chen J., Huisinga K.L., Viering M.M., et al. Enhancer action in trans is permitted throughout the Drosophila genome. Proc. Natl. Acad. Sci. USA 2002, 99:3723-3728.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 3723-3728
    • Chen, J.1    Huisinga, K.L.2    Viering, M.M.3
  • 39
    • 0347914543 scopus 로고    scopus 로고
    • The core enhancer is essential for proper timing of Myod activation in limb buds and branchial arches
    • Chen J.C.J., Goldhamer D.J. The core enhancer is essential for proper timing of Myod activation in limb buds and branchial arches. Dev. Biol. 2004, 265:502-512.
    • (2004) Dev. Biol. , vol.265 , pp. 502-512
    • Chen, J.C.J.1    Goldhamer, D.J.2
  • 40
    • 26444593024 scopus 로고    scopus 로고
    • Complex cardiac Nkx2-5 gene expression activated by noggin-sensitive enhancers followed by chamber-specific modules
    • Chi X., Chatterjee P.K., Wilson W., Zhang S., Demayo F.J., Schwartz R.J. Complex cardiac Nkx2-5 gene expression activated by noggin-sensitive enhancers followed by chamber-specific modules. Proc. Natl Acad. Sci. USA 2005, 102:13490-13495.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13490-13495
    • Chi, X.1    Chatterjee, P.K.2    Wilson, W.3    Zhang, S.4    Demayo, F.J.5    Schwartz, R.J.6
  • 41
    • 0028124772 scopus 로고
    • Mice with targeted disruptions in the paralogous genes Hoxa-3 and Hoxd-3 reveal synergistic interactions
    • Condie B.G., Capecchi M.R. Mice with targeted disruptions in the paralogous genes Hoxa-3 and Hoxd-3 reveal synergistic interactions. Nature 1994, 370:304-307.
    • (1994) Nature , vol.370 , pp. 304-307
    • Condie, B.G.1    Capecchi, M.R.2
  • 42
    • 0033529717 scopus 로고    scopus 로고
    • The Tra-1a sex determination protein of c. elegans regulates sexually dimorphic cell deaths by repressing the Egl-1 cell death activator gene
    • Conradt B., Horvitz H.R. The Tra-1a sex determination protein of c. elegans regulates sexually dimorphic cell deaths by repressing the Egl-1 cell death activator gene. Cell 1999, 98:317-327.
    • (1999) Cell , vol.98 , pp. 317-327
    • Conradt, B.1    Horvitz, H.R.2
  • 43
    • 37449026431 scopus 로고    scopus 로고
    • Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain
    • Conte I., Bovolenta P. Comprehensive characterization of the cis-regulatory code responsible for the spatio-temporal expression of olSix3.2 in the developing medaka forebrain. Genome Biol. 2007, 8:R137.
    • (2007) Genome Biol. , vol.8
    • Conte, I.1    Bovolenta, P.2
  • 44
    • 39449101500 scopus 로고    scopus 로고
    • Microchip-a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies
    • Dahl J.A., Collas P. Microchip-a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies. Nucleic Acids Res. 2008, 36:e15.
    • (2008) Nucleic Acids Res. , vol.36
    • Dahl, J.A.1    Collas, P.2
  • 45
    • 64149103056 scopus 로고    scopus 로고
    • Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type a2
    • Dathe K., Kjaer K.W., Brehm A., et al. Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type a2. Am. J. Hum. Genet. 2009, 84:483-492.
    • (2009) Am. J. Hum. Genet. , vol.84 , pp. 483-492
    • Dathe, K.1    Kjaer, K.W.2    Brehm, A.3
  • 47
    • 23744502709 scopus 로고    scopus 로고
    • A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate iroquois cluster gene deserts
    • de la Calle-Mustienes E., Feijóo C.G., Manzanares M., et al. A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate iroquois cluster gene deserts. Genome Res. 2005, 15:1061-1072.
    • (2005) Genome Res. , vol.15 , pp. 1061-1072
    • de la Calle-Mustienes, E.1    Feijóo, C.G.2    Manzanares, M.3
  • 49
    • 0037083376 scopus 로고    scopus 로고
    • Capturing chromosome conformation
    • Dekker J., Rippe K., Dekker M., et al. Capturing chromosome conformation. Science 2002, 295:1306-1311.
    • (2002) Science , vol.295 , pp. 1306-1311
    • Dekker, J.1    Rippe, K.2    Dekker, M.3
  • 50
    • 34250369629 scopus 로고    scopus 로고
    • Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
    • Denoeud F., Kapranov P., Ucla C., et al. Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007, 17:746-759.
    • (2007) Genome Res. , vol.17 , pp. 746-759
    • Denoeud, F.1    Kapranov, P.2    Ucla, C.3
  • 51
    • 0242662461 scopus 로고    scopus 로고
    • Evolutionary discrimination of mammalian conserved non-genic sequences (cngs)
    • Dermitzakis E.T., Reymond A., Scamuffa N., et al. Evolutionary discrimination of mammalian conserved non-genic sequences (cngs). Science 2003, 302:1033-1035.
    • (2003) Science , vol.302 , pp. 1033-1035
    • Dermitzakis, E.T.1    Reymond, A.2    Scamuffa, N.3
  • 52
    • 70350029560 scopus 로고    scopus 로고
    • Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
    • Dong X., Fredman D., Lenhard B. Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes. Genome Biol. 2009, 10:R86.
    • (2009) Genome Biol. , vol.10
    • Dong, X.1    Fredman, D.2    Lenhard, B.3
  • 54
    • 0027296569 scopus 로고
    • Distance-independent inactivation of an enhancer by the suppressor of hairy-wing DNA-binding protein of Drosophila
    • Dorsett D. Distance-independent inactivation of an enhancer by the suppressor of hairy-wing DNA-binding protein of Drosophila. Genetics 1993, 134:1135-1144.
    • (1993) Genetics , vol.134 , pp. 1135-1144
    • Dorsett, D.1
  • 55
    • 33749400168 scopus 로고    scopus 로고
    • Chromosome conformation capture carbon copy (5c): a massively parallel solution for mapping interactions between genomic elements
    • Dostie J., Richmond T.A., Arnaout R.A., et al. Chromosome conformation capture carbon copy (5c): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006, 16:1299-1309.
    • (2006) Genome Res. , vol.16 , pp. 1299-1309
    • Dostie, J.1    Richmond, T.A.2    Arnaout, R.A.3
  • 56
    • 31744448843 scopus 로고    scopus 로고
    • Conserved noncoding sequences are selectively constrained and not mutation cold spots
    • Drake J.A., Bird C., Nemesh J., et al. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat. Genet. 2006, 38:223-227.
    • (2006) Nat. Genet. , vol.38 , pp. 223-227
    • Drake, J.A.1    Bird, C.2    Nemesh, J.3
  • 57
    • 0033799618 scopus 로고    scopus 로고
    • Active conservation of noncoding sequences revealed by three-way species comparisons
    • Dubchak I., Brudno M., Loots G.G., et al. Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res. 2000, 10:1304-1306.
    • (2000) Genome Res. , vol.10 , pp. 1304-1306
    • Dubchak, I.1    Brudno, M.2    Loots, G.G.3
  • 58
    • 67349226099 scopus 로고    scopus 로고
    • A toolkit for high-throughput, cross-species gene engineering in Drosophila
    • Ejsmont R.K., Sarov M., Winkler S., et al. A toolkit for high-throughput, cross-species gene engineering in Drosophila. Nat. Methods 2009.
    • (2009) Nat. Methods
    • Ejsmont, R.K.1    Sarov, M.2    Winkler, S.3
  • 59
    • 33845341455 scopus 로고    scopus 로고
    • Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques
    • Elnitski L., Jin V.X., Farnham P.J., et al. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res. 2006, 16:1455-1464.
    • (2006) Genome Res. , vol.16 , pp. 1455-1464
    • Elnitski, L.1    Jin, V.X.2    Farnham, P.J.3
  • 60
    • 38849112675 scopus 로고    scopus 로고
    • Genomic regulatory blocks underlie extensive microsynteny conservation in insects
    • Engström P.G., Ho Sui S.J., Drivenes O., et al. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Res. 2007, 17:1898-1908.
    • (2007) Genome Res. , vol.17 , pp. 1898-1908
    • Engström, P.G.1    Ho Sui, S.J.2    Drivenes, O.3
  • 61
    • 33846087787 scopus 로고    scopus 로고
    • Cooperation of sonic hedgehog enhancers in midline expression
    • Ertzer R., Müller F., Hadzhiev Y., et al. Cooperation of sonic hedgehog enhancers in midline expression. Dev. Biol. 2007, 301:578-589.
    • (2007) Dev. Biol. , vol.301 , pp. 578-589
    • Ertzer, R.1    Müller, F.2    Hadzhiev, Y.3
  • 64
    • 39749149956 scopus 로고    scopus 로고
    • Housekeeping genes tend to show reduced upstream sequence conservation
    • Farré D., Bellora N., Mularoni L., et al. Housekeeping genes tend to show reduced upstream sequence conservation. Genome Biol. 2007, 8:R140.
    • (2007) Genome Biol. , vol.8
    • Farré, D.1    Bellora, N.2    Mularoni, L.3
  • 65
    • 33744804277 scopus 로고    scopus 로고
    • The evf-2 noncoding RNA is transcribed from the dlx-5/6 ultraconserved region and functions as a dlx-2 transcriptional coactivator
    • Feng J., Bi C., Clark B.S., et al. The evf-2 noncoding RNA is transcribed from the dlx-5/6 ultraconserved region and functions as a dlx-2 transcriptional coactivator. Genes Dev. 2006, 20:1470-1484.
    • (2006) Genes Dev. , vol.20 , pp. 1470-1484
    • Feng, J.1    Bi, C.2    Clark, B.S.3
  • 66
    • 33645833857 scopus 로고    scopus 로고
    • Conservation of RET regulatory function from human to zebrafish without sequence similarity
    • Fisher S., Grice E.A., Vinton R.M., et al. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 2006, 312:276-279.
    • (2006) Science , vol.312 , pp. 276-279
    • Fisher, S.1    Grice, E.A.2    Vinton, R.M.3
  • 67
    • 0028258384 scopus 로고
    • Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome iii
    • Fondrat C., Kalogeropoulos A. Approaching the function of new genes by detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome iii. Curr. Genet. 1994, 25:396-406.
    • (1994) Curr. Genet. , vol.25 , pp. 396-406
    • Fondrat, C.1    Kalogeropoulos, A.2
  • 68
    • 0025107556 scopus 로고
    • A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus
    • Forrester W.C., Epner E., Driscoll M.C., Enver T., Brice M., Papayannopoulou T., Groudine M. A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus. Genes Dev. 1990, 4:1637-1649.
    • (1990) Genes Dev. , vol.4 , pp. 1637-1649
    • Forrester, W.C.1    Epner, E.2    Driscoll, M.C.3    Enver, T.4    Brice, M.5    Papayannopoulou, T.6    Groudine, M.7
  • 69
    • 38049020974 scopus 로고    scopus 로고
    • A code for transcription initiation in mammalian genomes
    • Frith M.C., Valen E., Krogh A., et al. A code for transcription initiation in mammalian genomes. Genome Res. 2008, 18:1-12.
    • (2008) Genome Res. , vol.18 , pp. 1-12
    • Frith, M.C.1    Valen, E.2    Krogh, A.3
  • 70
    • 0036468361 scopus 로고    scopus 로고
    • Regulation of organogenesis by the Caenorhabditis elegans Foxa protein pha-4
    • Gaudet J., Mango S.E. Regulation of organogenesis by the Caenorhabditis elegans Foxa protein pha-4. Science 2002, 295:821-825.
    • (2002) Science , vol.295 , pp. 821-825
    • Gaudet, J.1    Mango, S.E.2
  • 72
    • 58149354385 scopus 로고    scopus 로고
    • Analysis of combinatorial cis-regulation in synthetic and genomic promoters
    • Gertz J., Siggia E.D., Cohen B.A. Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 2009, 457:215-218.
    • (2009) Nature , vol.457 , pp. 215-218
    • Gertz, J.1    Siggia, E.D.2    Cohen, B.A.3
  • 73
    • 1642432069 scopus 로고    scopus 로고
    • GENSAT: a genomic resource for neuroscience research
    • Geschwind D. GENSAT: a genomic resource for neuroscience research. Lancet Neurol. 2004, 3:82.
    • (2004) Lancet Neurol. , vol.3 , pp. 82
    • Geschwind, D.1
  • 75
    • 34248326896 scopus 로고    scopus 로고
    • Distinct cis-regulatory elements from the Dlx1/Dlx2 locus mark different progenitor cell populations in the ganglionic eminences and different subtypes of adult cortical interneurons
    • Ghanem N., Yu M., Long J., Hatch G., Rubenstein J.L.R., Ekker M. Distinct cis-regulatory elements from the Dlx1/Dlx2 locus mark different progenitor cell populations in the ganglionic eminences and different subtypes of adult cortical interneurons. J. Neurosci. Off. J. Soc. Neurosci. 2007, 27:5012-5022.
    • (2007) J. Neurosci. Off. J. Soc. Neurosci. , vol.27 , pp. 5012-5022
    • Ghanem, N.1    Yu, M.2    Long, J.3    Hatch, G.4    Rubenstein, J.L.R.5    Ekker, M.6
  • 76
    • 77955235716 scopus 로고    scopus 로고
    • Cell-type-specific long-range looping interactions identify distant regulatory elements of the cftr gene
    • Gheldof N., Smith E.M., Tabuchi T.M., et al. Cell-type-specific long-range looping interactions identify distant regulatory elements of the cftr gene. Nucleic Acids Res. 2010, 38:4325-4336.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4325-4336
    • Gheldof, N.1    Smith, E.M.2    Tabuchi, T.M.3
  • 77
    • 22344454794 scopus 로고    scopus 로고
    • Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
    • Glazov E.A., Pheasant M., McGraw E.A., Bejerano G., Mattick J.S. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res. 2005, 15:800-808.
    • (2005) Genome Res. , vol.15 , pp. 800-808
    • Glazov, E.A.1    Pheasant, M.2    McGraw, E.A.3    Bejerano, G.4    Mattick, J.S.5
  • 78
    • 21444434589 scopus 로고    scopus 로고
    • Highly conserved regulatory elements around the shh gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3
    • Goode D.K., Snell P., Smith S.F., et al. Highly conserved regulatory elements around the shh gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3. Genomics 2005, 86:172-181.
    • (2005) Genomics , vol.86 , pp. 172-181
    • Goode, D.K.1    Snell, P.2    Smith, S.F.3
  • 79
    • 77951266764 scopus 로고    scopus 로고
    • Finding regulatory DNA motifs using alignment-free evolutionary conservation information
    • Gordân R., Narlikar L., Hartemink A.J. Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Res. 2010.
    • (2010) Nucleic Acids Res.
    • Gordân, R.1    Narlikar, L.2    Hartemink, A.J.3
  • 81
    • 49449107340 scopus 로고    scopus 로고
    • Visualizing one-dimensional diffusion of proteins along DNA
    • Gorman J., Greene E.C. Visualizing one-dimensional diffusion of proteins along DNA. Nat. Struct. Mol. Biol. 2008, 15:768-774.
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 768-774
    • Gorman, J.1    Greene, E.C.2
  • 82
    • 77951874066 scopus 로고    scopus 로고
    • Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
    • Gotea V., Visel A., Westlund J.M., et al. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res. 2010, 20:565-577.
    • (2010) Genome Res. , vol.20 , pp. 565-577
    • Gotea, V.1    Visel, A.2    Westlund, J.M.3
  • 83
    • 0033972132 scopus 로고    scopus 로고
    • Analysis of vertebrate scl loci identifies conserved enhancers
    • Göttgens B., Barton L.M., Gilbert J.G., et al. Analysis of vertebrate scl loci identifies conserved enhancers. Nat. Biotechnol. 2000, 18:181-186.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 181-186
    • Göttgens, B.1    Barton, L.M.2    Gilbert, J.G.3
  • 84
    • 38549087902 scopus 로고    scopus 로고
    • ORegAnno: an open-access community-driven resource for regulatory annotation
    • Griffith O.L., Montgomery S.B., Bernier B., et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res. 2008, 36:D107-D113.
    • (2008) Nucleic Acids Res. , vol.36
    • Griffith, O.L.1    Montgomery, S.B.2    Bernier, B.3
  • 85
    • 0023899769 scopus 로고
    • Nuclease hypersensitive sites in chromatin
    • Gross D.S., Garrard W.T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 1988, 57:159-197.
    • (1988) Annu. Rev. Biochem. , vol.57 , pp. 159-197
    • Gross, D.S.1    Garrard, W.T.2
  • 86
    • 70450221669 scopus 로고    scopus 로고
    • Secondary enhancers synergise with primary enhancers to guarantee fine-tuned muscle gene expression
    • Guerrero L., Marco-Ferreres R., Serrano A.L., Arredondo J.J., Cervera M. Secondary enhancers synergise with primary enhancers to guarantee fine-tuned muscle gene expression. Dev. Biol. 2010, 337:16-28.
    • (2010) Dev. Biol. , vol.337 , pp. 16-28
    • Guerrero, L.1    Marco-Ferreres, R.2    Serrano, A.L.3    Arredondo, J.J.4    Cervera, M.5
  • 87
    • 39649102569 scopus 로고    scopus 로고
    • A short ultraconserved sequence drives transcription from an alternate Fbn1 promoter
    • Guo G., Bauer S., Hecht J., et al. A short ultraconserved sequence drives transcription from an alternate Fbn1 promoter. Int. J. Biochem. Cell Biol. 2008, 40:638-650.
    • (2008) Int. J. Biochem. Cell Biol. , vol.40 , pp. 638-650
    • Guo, G.1    Bauer, S.2    Hecht, J.3
  • 88
    • 3042705860 scopus 로고    scopus 로고
    • Deletion of the major Gata1 enhancer hs 1 does not affect eosinophil Gata1 expression and eosinophil differentiation
    • Guyot B., Valverde-Garduno V., Porcher C., et al. Deletion of the major Gata1 enhancer hs 1 does not affect eosinophil Gata1 expression and eosinophil differentiation. Blood 2004, 104:89-91.
    • (2004) Blood , vol.104 , pp. 89-91
    • Guyot, B.1    Valverde-Garduno, V.2    Porcher, C.3
  • 89
    • 77952325730 scopus 로고    scopus 로고
    • A cis-regulatory signature for chordate anterior neurectodermal genes
    • Haeussler M., Jaszczyszyn Y., Christiaen L., Joly J.S. A cis-regulatory signature for chordate anterior neurectodermal genes. PLoS Genet. 2010, 6:e1000912.
    • (2010) PLoS Genet. , vol.6
    • Haeussler, M.1    Jaszczyszyn, Y.2    Christiaen, L.3    Joly, J.S.4
  • 90
    • 38549105493 scopus 로고    scopus 로고
    • Redfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila
    • Halfon M.S., Gallo S.M., Bergman C.M. Redfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila. Nucleic Acids Res. 2008, 36:D594-D598.
    • (2008) Nucleic Acids Res. , vol.36
    • Halfon, M.S.1    Gallo, S.M.2    Bergman, C.M.3
  • 91
    • 0028206856 scopus 로고
    • Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen
    • Hanes S.D., Riddihough G., Ish-Horowicz D., et al. Specific DNA recognition and intersite spacing are critical for action of the bicoid morphogen. Mol. Cell. Biol. 1994, 14:3364-3375.
    • (1994) Mol. Cell. Biol. , vol.14 , pp. 3364-3375
    • Hanes, S.D.1    Riddihough, G.2    Ish-Horowicz, D.3
  • 92
    • 30344439849 scopus 로고    scopus 로고
    • Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity
    • Hallikas O., Palin K., Sinjushina N., et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 2006, 124:47-59.
    • (2006) Cell , vol.124 , pp. 47-59
    • Hallikas, O.1    Palin, K.2    Sinjushina, N.3
  • 93
    • 4544352942 scopus 로고    scopus 로고
    • Transcriptional regulatory code of a eukaryotic genome
    • Harbison C.T., Gordon D.B., Lee T.I., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104.
    • (2004) Nature , vol.431 , pp. 99-104
    • Harbison, C.T.1    Gordon, D.B.2    Lee, T.I.3
  • 94
    • 0027497513 scopus 로고
    • Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters
    • Hardison R., Miller W. Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters. Mol. Biol. Evol. 1993, 10:73-102.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 73-102
    • Hardison, R.1    Miller, W.2
  • 95
    • 0030722935 scopus 로고    scopus 로고
    • Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome
    • Hardison R.C., Oeltjen J., Miller W. Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res. 1997, 7:959-966.
    • (1997) Genome Res. , vol.7 , pp. 959-966
    • Hardison, R.C.1    Oeltjen, J.2    Miller, W.3
  • 96
    • 57149097264 scopus 로고    scopus 로고
    • A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids
    • Hare E.E., Peterson B.K., Eisen M.B. A careful look at binding site reorganization in the even-skipped enhancers of Drosophila and sepsids. PLoS Genet. 2008, 4:e1000268.
    • (2008) PLoS Genet. , vol.4
    • Hare, E.E.1    Peterson, B.K.2    Eisen, M.B.3
  • 97
    • 46249134068 scopus 로고    scopus 로고
    • Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
    • Hare E.E., Peterson B.K., Iyer V.N., et al. Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet. 2008, 4:e1000106.
    • (2008) PLoS Genet. , vol.4
    • Hare, E.E.1    Peterson, B.K.2    Iyer, V.N.3
  • 98
    • 77950262538 scopus 로고    scopus 로고
    • Nucleosome dynamics define transcriptional enhancers
    • He H.H., Meyer C.A., Shin H., et al. Nucleosome dynamics define transcriptional enhancers. Nat. Genet. 2010, 42:343-347.
    • (2010) Nat. Genet. , vol.42 , pp. 343-347
    • He, H.H.1    Meyer, C.A.2    Shin, H.3
  • 99
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifications at human enhancers reflect global cell-type-specific gene expression
    • Heintzman N.D., Hon G.C., Hawkins R.D., et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009, 459:108-112.
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1    Hon, G.C.2    Hawkins, R.D.3
  • 100
    • 0036214657 scopus 로고    scopus 로고
    • PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans
    • Hobert O. PCR fusion-based approach to create reporter gene constructs for expression analysis in transgenic C. elegans. Biotechniques 2002, 32:728-730.
    • (2002) Biotechniques , vol.32 , pp. 728-730
    • Hobert, O.1
  • 101
    • 58149484991 scopus 로고    scopus 로고
    • Regulatory logic of neuronal diversity: terminal selector genes and selector motifs
    • Hobert O. Regulatory logic of neuronal diversity: terminal selector genes and selector motifs. Proc. Natl. Acad. Sci. USA 2008, 105:20067-20071.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 20067-20071
    • Hobert, O.1
  • 102
    • 51149097760 scopus 로고    scopus 로고
    • Shadow enhancers as a source of evolutionary novelty
    • Hong J., Hendrix D.A., Levine M.S. Shadow enhancers as a source of evolutionary novelty. Science 2008, 321:1314.
    • (2008) Science , vol.321 , pp. 1314
    • Hong, J.1    Hendrix, D.A.2    Levine, M.S.3
  • 103
    • 0029045063 scopus 로고
    • Mutations in paralogous HOX genes result in overlapping homeotic transformations of the axial skeleton: evidence for unique and redundant function
    • Horan G.S., Kovàcs E.N., Behringer R.R., et al. Mutations in paralogous HOX genes result in overlapping homeotic transformations of the axial skeleton: evidence for unique and redundant function. Dev. Biol. 1995, 169:359-372.
    • (1995) Dev. Biol. , vol.169 , pp. 359-372
    • Horan, G.S.1    Kovàcs, E.N.2    Behringer, R.R.3
  • 104
    • 48349124629 scopus 로고    scopus 로고
    • MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs
    • Hu J., Hu H., Li X. MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs. Nucleic Acids Res. 2008, 36:4488-4497.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 4488-4497
    • Hu, J.1    Hu, H.2    Li, X.3
  • 105
    • 70350741353 scopus 로고    scopus 로고
    • Deeply conserved chordate non-coding sequences preserve genome synteny but do not drive gene duplicate retention
    • Hufton A.L., Mathia S., Braun H., et al. Deeply conserved chordate non-coding sequences preserve genome synteny but do not drive gene duplicate retention. Genome Res. 2009, 19:2036-2051.
    • (2009) Genome Res. , vol.19 , pp. 2036-2051
    • Hufton, A.L.1    Mathia, S.2    Braun, H.3
  • 106
    • 43049107466 scopus 로고    scopus 로고
    • Cis-regulatory organization of the Pax6 gene in the ascidian Ciona intestinalis
    • Irvine S.Q., Fonseca V.C., Zompa M.A., et al. Cis-regulatory organization of the Pax6 gene in the ascidian Ciona intestinalis. Dev. Biol. 2008, 317:649-659.
    • (2008) Dev. Biol. , vol.317 , pp. 649-659
    • Irvine, S.Q.1    Fonseca, V.C.2    Zompa, M.A.3
  • 108
    • 46249100442 scopus 로고    scopus 로고
    • Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs
    • Ivan A., Halfon M.S., Sinha S. Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol. 2008, 9:R22.
    • (2008) Genome Biol. , vol.9
    • Ivan, A.1    Halfon, M.S.2    Sinha, S.3
  • 109
    • 2942556997 scopus 로고    scopus 로고
    • A conserved enhancer element that drives Fgf4 gene expression in the embryonic myotomes is synergistically activated by gata and bhlh proteins
    • Iwahori A., Fraidenraich D., Basilico C. A conserved enhancer element that drives Fgf4 gene expression in the embryonic myotomes is synergistically activated by gata and bhlh proteins. Dev. Biol. 2004, 270:525-537.
    • (2004) Dev. Biol. , vol.270 , pp. 525-537
    • Iwahori, A.1    Fraidenraich, D.2    Basilico, C.3
  • 111
    • 0025943096 scopus 로고
    • Expression of the cut locus in the Drosophila wing margin is required for cell type specification and is regulated by a distant enhancer
    • Jack J., Dorsett D., Delotto Y., et al. Expression of the cut locus in the Drosophila wing margin is required for cell type specification and is regulated by a distant enhancer. Development 1991, 113:735-747.
    • (1991) Development , vol.113 , pp. 735-747
    • Jack, J.1    Dorsett, D.2    Delotto, Y.3
  • 112
    • 33749137281 scopus 로고    scopus 로고
    • Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene
    • Janssens H., Hou S., Jaeger J., et al. Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat. Genet. 2006, 38:1159-1165.
    • (2006) Nat. Genet. , vol.38 , pp. 1159-1165
    • Janssens, H.1    Hou, S.2    Jaeger, J.3
  • 113
    • 43549109877 scopus 로고    scopus 로고
    • Isolation of neuronal chromatin from brain tissue
    • Jiang Y., Matevossian A., Huang H., et al. Isolation of neuronal chromatin from brain tissue. BMC Neurosci. 2008, 9:42.
    • (2008) BMC Neurosci. , vol.9 , pp. 42
    • Jiang, Y.1    Matevossian, A.2    Huang, H.3
  • 114
    • 28244474539 scopus 로고    scopus 로고
    • Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster
    • Jones E.A., Flavell R.A. Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster. J. Immunol. 2005, 175:7437-7446.
    • (2005) J. Immunol. , vol.175 , pp. 7437-7446
    • Jones, E.A.1    Flavell, R.A.2
  • 115
    • 0142212148 scopus 로고    scopus 로고
    • Enhancer timing of HOX gene expression: deletion of the endogenous HOXC8 early enhancer
    • Juan A.H., Ruddle F.H. Enhancer timing of HOX gene expression: deletion of the endogenous HOXC8 early enhancer. Development 2003, 130:4823-4834.
    • (2003) Development , vol.130 , pp. 4823-4834
    • Juan, A.H.1    Ruddle, F.H.2
  • 116
    • 77149174487 scopus 로고    scopus 로고
    • Regulation of gene expression via the core promoter and the basal transcriptional machinery
    • Juven-Gershon T., Kadonaga J.T. Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev. Biol. 2010, 339:225-229.
    • (2010) Dev. Biol. , vol.339 , pp. 225-229
    • Juven-Gershon, T.1    Kadonaga, J.T.2
  • 117
    • 33750345805 scopus 로고    scopus 로고
    • Rational design of a super core promoter that enhances gene expression
    • Juven-Gershon T., Cheng S., Kadonaga J.T. Rational design of a super core promoter that enhances gene expression. Nat. Methods 2006, 3:917-922.
    • (2006) Nat. Methods , vol.3 , pp. 917-922
    • Juven-Gershon, T.1    Cheng, S.2    Kadonaga, J.T.3
  • 119
    • 70349996336 scopus 로고    scopus 로고
    • Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse
    • Kantorovitz M.R., Kazemian M., Kinston S., et al. Motif-blind, genome-wide discovery of cis-regulatory modules in Drosophila and mouse. Dev. Cell 2009, 17:568-579.
    • (2009) Dev. Cell , vol.17 , pp. 568-579
    • Kantorovitz, M.R.1    Kazemian, M.2    Kinston, S.3
  • 122
    • 15744388330 scopus 로고    scopus 로고
    • Evidence for widespread degradation of gene control regions in hominid genomes
    • Keightley P.D., Lercher M.J., Eyre-Walker A. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 2005, 3:e42.
    • (2005) PLoS Biol. , vol.3
    • Keightley, P.D.1    Lercher, M.J.2    Eyre-Walker, A.3
  • 123
    • 0344824015 scopus 로고    scopus 로고
    • Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents
    • Keightley P.D., Gaffney D.J. Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc. Natl. Acad. Sci. USA 2003, 100:13402-13406.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13402-13406
    • Keightley, P.D.1    Gaffney, D.J.2
  • 124
    • 0036079158 scopus 로고    scopus 로고
    • The human genome browser at UCSC
    • Kent W.J., Sugnet C.W., Furey T.S., et al. The human genome browser at UCSC. Genome Res. 2002, 12:996-1006.
    • (2002) Genome Res. , vol.12 , pp. 996-1006
    • Kent, W.J.1    Sugnet, C.W.2    Furey, T.S.3
  • 125
    • 20044394526 scopus 로고    scopus 로고
    • A saturation screen for cis-acting regulatory DNA in the hox genes of ciona intestinalis
    • Keys D.N., Lee B., Di Gregorio A., et al. A saturation screen for cis-acting regulatory DNA in the hox genes of ciona intestinalis. Proc. Natl. Acad. Sci. USA 2005, 102:679-683.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 679-683
    • Keys, D.N.1    Lee, B.2    Di Gregorio, A.3
  • 126
    • 8644243022 scopus 로고    scopus 로고
    • Multiple, distant Gata2 enhancers specify temporally and tissue-specific patterning in the developing urogenital system
    • Khandekar M., Suzuki N., Lewton J., Yamamoto M., Engel J.D. Multiple, distant Gata2 enhancers specify temporally and tissue-specific patterning in the developing urogenital system. Mol. Cell. Biol. 2004, 24:10263-10276.
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 10263-10276
    • Khandekar, M.1    Suzuki, N.2    Lewton, J.3    Yamamoto, M.4    Engel, J.D.5
  • 127
    • 38449118642 scopus 로고    scopus 로고
    • Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes
    • Kikuta H., Fredman D., Rinkwitz S., et al. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol. 2007, 8(Suppl. 1):S4.
    • (2007) Genome Biol. , vol.8 , Issue.SUPPL. 1
    • Kikuta, H.1    Fredman, D.2    Rinkwitz, S.3
  • 128
    • 33947201809 scopus 로고    scopus 로고
    • Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
    • Kim T.H., Abdullaev Z.K., Smith A.D., et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128:1231-1245.
    • (2007) Cell , vol.128 , pp. 1231-1245
    • Kim, T.H.1    Abdullaev, Z.K.2    Smith, A.D.3
  • 129
    • 77952367798 scopus 로고    scopus 로고
    • Widespread transcription at neuronal activity-regulated enhancers
    • Kim T., Hemberg M., Gray J.M., et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 2010, 465:182-187.
    • (2010) Nature , vol.465 , pp. 182-187
    • Kim, T.1    Hemberg, M.2    Gray, J.M.3
  • 131
    • 34250358295 scopus 로고    scopus 로고
    • Finding cis-regulatory elements using comparative genomics: some lessons from encode data
    • King D.C., Taylor J., Zhang Y., et al. Finding cis-regulatory elements using comparative genomics: some lessons from encode data. Genome Res. 2007, 17:775-786.
    • (2007) Genome Res. , vol.17 , pp. 775-786
    • King, D.C.1    Taylor, J.2    Zhang, Y.3
  • 132
    • 0029817680 scopus 로고    scopus 로고
    • Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples
    • Kirchhamer C.V., Yuh C.H., Davidson E.H. Modular cis-regulatory organization of developmentally expressed genes: two genes transcribed territorially in the sea urchin embryo, and additional examples. Proc. Natl Acad. Sci. USA 1996, 93:9322-9328.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 9322-9328
    • Kirchhamer, C.V.1    Yuh, C.H.2    Davidson, E.H.3
  • 133
    • 70349611559 scopus 로고    scopus 로고
    • Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease
    • Kleinjan D., Coutinho P. Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease. Brief. Funct. Genomics Proteomics 2009, 8:317-332.
    • (2009) Brief. Funct. Genomics Proteomics , vol.8 , pp. 317-332
    • Kleinjan, D.1    Coutinho, P.2
  • 134
    • 0347914540 scopus 로고    scopus 로고
    • Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription
    • Kleinjan D.A., Seawright A., Childs A.J., van Heyningen V. Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription. Dev. Biol. 2004, 265:462-477.
    • (2004) Dev. Biol. , vol.265 , pp. 462-477
    • Kleinjan, D.A.1    Seawright, A.2    Childs, A.J.3    van Heyningen, V.4
  • 135
    • 34547919214 scopus 로고    scopus 로고
    • Real-time monitoring of functional interactions between upstream and core promoter sequences in living cells of sea urchin embryos
    • Kobayashi A., Watanabe Y., Akasaka K., et al. Real-time monitoring of functional interactions between upstream and core promoter sequences in living cells of sea urchin embryos. Nucleic Acids Res. 2007, 35:4882-4894.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 4882-4894
    • Kobayashi, A.1    Watanabe, Y.2    Akasaka, K.3
  • 136
    • 0347765651 scopus 로고    scopus 로고
    • Information display by transcriptional enhancers
    • Kulkarni M.M., Arnosti D.N. Information display by transcriptional enhancers. Development 2003, 130:6569-6575.
    • (2003) Development , vol.130 , pp. 6569-6575
    • Kulkarni, M.M.1    Arnosti, D.N.2
  • 137
    • 76249090744 scopus 로고    scopus 로고
    • COMIT: identification of noncoding motifs under selection in coding sequences
    • Kural D., Ding Y., Wu J., Korpi A.M., Chuang J.H. COMIT: identification of noncoding motifs under selection in coding sequences. Genome Biol. 2009, 10:R133.
    • (2009) Genome Biol. , vol.10
    • Kural, D.1    Ding, Y.2    Wu, J.3    Korpi, A.M.4    Chuang, J.H.5
  • 138
    • 45549100203 scopus 로고    scopus 로고
    • An ultraconserved hox-pbx responsive element resides in the coding sequence of hoxa2 and is active in rhombomere 4
    • Lampe X., Samad O.A., Guiguen A., et al. An ultraconserved hox-pbx responsive element resides in the coding sequence of hoxa2 and is active in rhombomere 4. Nucleic Acids Res. 2008, 36:3214-3225.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3214-3225
    • Lampe, X.1    Samad, O.A.2    Guiguen, A.3
  • 139
    • 33845742990 scopus 로고    scopus 로고
    • Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions
    • Lee A.M., Wu C. Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions. Genetics 2006, 174:1867-1880.
    • (2006) Genetics , vol.174 , pp. 1867-1880
    • Lee, A.M.1    Wu, C.2
  • 140
    • 33646468497 scopus 로고    scopus 로고
    • Highly conserved syntenic blocks at the vertebrate hox loci and conserved regulatory elements within and outside hox gene clusters
    • Lee A.P., Koh E.G.L., Tay A., et al. Highly conserved syntenic blocks at the vertebrate hox loci and conserved regulatory elements within and outside hox gene clusters. Proc. Natl. Acad. Sci. USA 2006, 103:6994-6999.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 6994-6999
    • Lee, A.P.1    Koh, E.G.L.2    Tay, A.3
  • 141
    • 38549182460 scopus 로고    scopus 로고
    • Web resources for c. elegans studies
    • Lee R. Web resources for c. elegans studies. WormBook 2005, 1-16.
    • (2005) WormBook , pp. 1-16
    • Lee, R.1
  • 142
    • 0042810698 scopus 로고    scopus 로고
    • A long-range shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly
    • Lettice L.A., Heaney S.J.H., Purdie L.A., et al. A long-range shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 2003, 12:1725-1735.
    • (2003) Hum. Mol. Genet. , vol.12 , pp. 1725-1735
    • Lettice, L.A.1    Heaney, S.J.H.2    Purdie, L.A.3
  • 143
    • 41149157070 scopus 로고    scopus 로고
    • Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly
    • Lettice L.A., Hill A.E., Devenney P.S., et al. Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly. Hum. Mol. Genet. 2008, 17:978-985.
    • (2008) Hum. Mol. Genet. , vol.17 , pp. 978-985
    • Lettice, L.A.1    Hill, A.E.2    Devenney, P.S.3
  • 144
    • 0033987611 scopus 로고    scopus 로고
    • Two Pax2/5/8-binding sites in Engrailed2 are required for proper initiation of endogenous mid-hindbrain expression
    • Li Song D., Joyner A.L. Two Pax2/5/8-binding sites in Engrailed2 are required for proper initiation of endogenous mid-hindbrain expression. Mech. Dev. 2000, 90:155-165.
    • (2000) Mech. Dev. , vol.90 , pp. 155-165
    • Li Song, D.1    Joyner, A.L.2
  • 145
    • 33645887244 scopus 로고    scopus 로고
    • Chromatin looping and the probability of transcription
    • Li Q., Barkess G., Qian H. Chromatin looping and the probability of transcription. Trends Genet. 2006, 22:197-202.
    • (2006) Trends Genet. , vol.22 , pp. 197-202
    • Li, Q.1    Barkess, G.2    Qian, H.3
  • 146
    • 0028123693 scopus 로고
    • Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo
    • Li X., Noll M. Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo. EMBO J. 1994, 13:400-406.
    • (1994) EMBO J. , vol.13 , pp. 400-406
    • Li, X.1    Noll, M.2
  • 147
    • 40149095913 scopus 로고    scopus 로고
    • Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
    • Li X., MacArthur S., Bourgon R., et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008, 6:e27.
    • (2008) PLoS Biol. , vol.6
    • Li, X.1    MacArthur, S.2    Bourgon, R.3
  • 148
    • 57649220038 scopus 로고    scopus 로고
    • Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa l.) paralogous regions
    • Li X., Tan L., Wang L., et al. Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa l.) paralogous regions. Mol. Genet. Genomics 2009, 281:11-18.
    • (2009) Mol. Genet. Genomics , vol.281 , pp. 11-18
    • Li, X.1    Tan, L.2    Wang, L.3
  • 149
    • 38549168437 scopus 로고    scopus 로고
    • Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
    • Li L., Zhu Q., He X., et al. Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses. Genome Biol. 2007, 8:R101.
    • (2007) Genome Biol. , vol.8
    • Li, L.1    Zhu, Q.2    He, X.3
  • 150
    • 0037398319 scopus 로고    scopus 로고
    • Homotypic regulatory clusters in Drosophila
    • Lifanov A.P., Makeev V.J., Nazina A.G., et al. Homotypic regulatory clusters in Drosophila. Genome Res. 2003, 13:579-588.
    • (2003) Genome Res. , vol.13 , pp. 579-588
    • Lifanov, A.P.1    Makeev, V.J.2    Nazina, A.G.3
  • 151
    • 33746228114 scopus 로고    scopus 로고
    • Interchromosomal interactions and olfactory receptor choice
    • Lomvardas S., Barnea G., Pisapia D.J., et al. Interchromosomal interactions and olfactory receptor choice. Cell 2006, 126:403-413.
    • (2006) Cell , vol.126 , pp. 403-413
    • Lomvardas, S.1    Barnea, G.2    Pisapia, D.J.3
  • 152
    • 0030728460 scopus 로고    scopus 로고
    • Gata-1 expression pattern can be recapitulated in living transgenic zebrafish using gfp reporter gene
    • Long Q., Meng A., Wang H., et al. Gata-1 expression pattern can be recapitulated in living transgenic zebrafish using gfp reporter gene. Development 1997, 124:4105-4111.
    • (1997) Development , vol.124 , pp. 4105-4111
    • Long, Q.1    Meng, A.2    Wang, H.3
  • 153
    • 34447516953 scopus 로고    scopus 로고
    • Remote control of gene expression
    • Long X., Miano J.M. Remote control of gene expression. J. Biol. Chem. 2007, 282:15941-15945.
    • (2007) J. Biol. Chem. , vol.282 , pp. 15941-15945
    • Long, X.1    Miano, J.M.2
  • 154
    • 39049135380 scopus 로고    scopus 로고
    • Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis
    • Loots G.G. Genomic identification of regulatory elements by evolutionary sequence comparison and functional analysis. Adv. Genet. 2008, 61:269-293.
    • (2008) Adv. Genet. , vol.61 , pp. 269-293
    • Loots, G.G.1
  • 156
    • 33646229522 scopus 로고    scopus 로고
    • Practical strategies for discovering regulatory DNA sequence motifs
    • MacIsaac K.D., Fraenkel E. Practical strategies for discovering regulatory DNA sequence motifs. PLoS Comput. Biol. 2006, 2:e36.
    • (2006) PLoS Comput. Biol. , vol.2
    • MacIsaac, K.D.1    Fraenkel, E.2
  • 158
    • 35548971216 scopus 로고    scopus 로고
    • Making connections: boundaries and insulators in Drosophila
    • Maeda R.K., Karch F. Making connections: boundaries and insulators in Drosophila. Curr. Opin. Genet. Dev. 2007, 17:394-399.
    • (2007) Curr. Opin. Genet. Dev. , vol.17 , pp. 394-399
    • Maeda, R.K.1    Karch, F.2
  • 159
    • 0344442419 scopus 로고    scopus 로고
    • Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information
    • Makeev V.J., Lifanov A.P., Nazina A.G., et al. Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res. 2003, 31:6016-6026.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6016-6026
    • Makeev, V.J.1    Lifanov, A.P.2    Nazina, A.G.3
  • 160
    • 58549099738 scopus 로고    scopus 로고
    • ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes
    • Margolin A.A., Palomero T., Sumazin P., Califano A., Ferrando A.A., Stolovitzky G. ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes. Proc. Natl Acad. Sci. USA 2009, 106:244-249.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 244-249
    • Margolin, A.A.1    Palomero, T.2    Sumazin, P.3    Califano, A.4    Ferrando, A.A.5    Stolovitzky, G.6
  • 161
    • 0037154218 scopus 로고    scopus 로고
    • Genome-wide analysis of clustered dorsal binding sites identifies putative target genes in the Drosophila embryo
    • Markstein M., Markstein P., Markstein V., et al. 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.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 763-768
    • Markstein, M.1    Markstein, P.2    Markstein, V.3
  • 162
    • 41349092785 scopus 로고    scopus 로고
    • Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes
    • Markstein M., Pitsouli C., Villalta C., et al. Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes. Nat. Genet. 2008, 40:476-483.
    • (2008) Nat. Genet. , vol.40 , pp. 476-483
    • Markstein, M.1    Pitsouli, C.2    Villalta, C.3
  • 165
    • 34547569191 scopus 로고    scopus 로고
    • Stamp: a web tool for exploring DNA-binding motif similarities
    • Mahony S., Benos P.V. Stamp: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res. 2007, 35:W253-W258.
    • (2007) Nucleic Acids Res. , vol.35
    • Mahony, S.1    Benos, P.V.2
  • 167
    • 0037208166 scopus 로고    scopus 로고
    • Transfac: transcriptional regulation, from patterns to profiles
    • Matys V., Fricke E., Geffers R., et al. Transfac: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 2003, 31:374-378.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 374-378
    • Matys, V.1    Fricke, E.2    Geffers, R.3
  • 168
    • 33645519275 scopus 로고    scopus 로고
    • Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis
    • McEwen G.K., Woolfe A., Goode D., et al. Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis. Genome Res. 2006, 16:451-465.
    • (2006) Genome Res. , vol.16 , pp. 451-465
    • McEwen, G.K.1    Woolfe, A.2    Goode, D.3
  • 169
    • 39049147650 scopus 로고    scopus 로고
    • Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b
    • McGaughey D.M., Vinton R.M., Huynh J., et al. Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Res. 2008, 18:252-260.
    • (2008) Genome Res. , vol.18 , pp. 252-260
    • McGaughey, D.M.1    Vinton, R.M.2    Huynh, J.3
  • 170
    • 55549128249 scopus 로고    scopus 로고
    • Dispensability of mammalian DNA
    • McLean C., Bejerano G. Dispensability of mammalian DNA. Genome Res. 2008, 18:1743-1751.
    • (2008) Genome Res. , vol.18 , pp. 1743-1751
    • McLean, C.1    Bejerano, G.2
  • 171
    • 33746620028 scopus 로고    scopus 로고
    • An E box in the exon 1 promoter regulates Insulin-like Growth Factor-I expression in differentiating muscle cells
    • McLellan A.S., Kealey T., Langlands K. An E box in the exon 1 promoter regulates Insulin-like Growth Factor-I expression in differentiating muscle cells. Am. J. Physiol. Cell Physiol. 2006, 291:C300-C307.
    • (2006) Am. J. Physiol. Cell Physiol. , vol.291
    • McLellan, A.S.1    Kealey, T.2    Langlands, K.3
  • 172
    • 0029973108 scopus 로고    scopus 로고
    • Promoter specificity mediates the independent regulation of neighboring genes
    • Merli C., Bergstrom D.E., Cygan J.A., et al. Promoter specificity mediates the independent regulation of neighboring genes. Genes Dev. 1996, 10:1260-1270.
    • (1996) Genes Dev. , vol.10 , pp. 1260-1270
    • Merli, C.1    Bergstrom, D.E.2    Cygan, J.A.3
  • 173
    • 37849052436 scopus 로고    scopus 로고
    • Short sequence motifs, overrepresented in mammalian conserved non-coding sequences
    • Minovitsky S., Stegmaier P., Kel A., Kondrashov A.S., Dubchak I. Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. BMC Genomics 2007, 8:378.
    • (2007) BMC Genomics , vol.8 , pp. 378
    • Minovitsky, S.1    Stegmaier, P.2    Kel, A.3    Kondrashov, A.S.4    Dubchak, I.5
  • 174
    • 75149175733 scopus 로고    scopus 로고
    • Regulation of the p53 transcriptional response by structurally diverse core promoters
    • Morachis J.M., Murawsky C.M., Emerson B.M. Regulation of the p53 transcriptional response by structurally diverse core promoters. Genes Dev. 2010, 24:135-147.
    • (2010) Genes Dev. , vol.24 , pp. 135-147
    • Morachis, J.M.1    Murawsky, C.M.2    Emerson, B.M.3
  • 175
    • 77951972053 scopus 로고    scopus 로고
    • Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes
    • Muffato M., Louis A., Poisnel C.E., Crollius H.R. Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics 2010, 26:1119-1121.
    • (2010) Bioinformatics , vol.26 , pp. 1119-1121
    • Muffato, M.1    Louis, A.2    Poisnel, C.E.3    Crollius, H.R.4
  • 177
    • 60549097668 scopus 로고    scopus 로고
    • Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes
    • Navratilova P., Fredman D., Hawkins T.A., et al. Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes. Dev. Biol. 2009, 327:526-540.
    • (2009) Dev. Biol. , vol.327 , pp. 526-540
    • Navratilova, P.1    Fredman, D.2    Hawkins, T.A.3
  • 178
    • 4944260940 scopus 로고    scopus 로고
    • The regulatory content of intergenic DNA shapes genome architecture
    • Nelson C.E., Hersh B.M., Carroll S.B. The regulatory content of intergenic DNA shapes genome architecture. Genome Biol. 2004, 5:R25.
    • (2004) Genome Biol. , vol.5
    • Nelson, C.E.1    Hersh, B.M.2    Carroll, S.B.3
  • 179
    • 58149200952 scopus 로고    scopus 로고
    • UniPROBE: an online database of protein binding microarray data on protein-DNA interactions
    • Newburger D.E., Bulyk M.L. UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. Nucleic Acids Res. 2009, 37:D77-D82.
    • (2009) Nucleic Acids Res. , vol.37
    • Newburger, D.E.1    Bulyk, M.L.2
  • 181
    • 33745620751 scopus 로고    scopus 로고
    • Functional noncoding sequences derived from sines in the mammalian genome
    • Nishihara H., Smit A.F.A., Okada N. Functional noncoding sequences derived from sines in the mammalian genome. Genome Res. 2006, 16:864-874.
    • (2006) Genome Res. , vol.16 , pp. 864-874
    • Nishihara, H.1    Smit, A.F.A.2    Okada, N.3
  • 182
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • Nóbrega M.A., Ovcharenko I., Afzal V., Rubin E.M. Scanning human gene deserts for long-range enhancers. Science 2003, 302:413.
    • (2003) Science , vol.302 , pp. 413
    • Nóbrega, M.A.1    Ovcharenko, I.2    Afzal, V.3    Rubin, E.M.4
  • 183
    • 0348184969 scopus 로고    scopus 로고
    • Comparative genomic analysis as a tool for biological discovery
    • Nóbrega M.A., Pennacchio L.A. Comparative genomic analysis as a tool for biological discovery. J. Physiol. Lond. 2004, 554:31-39.
    • (2004) J. Physiol. Lond. , vol.554 , pp. 31-39
    • Nóbrega, M.A.1    Pennacchio, L.A.2
  • 184
    • 7244259100 scopus 로고    scopus 로고
    • Megabase deletions of gene deserts result in viable mice
    • Nóbrega M.A., Zhu Y., Plajzer-Frick I., et al. Megabase deletions of gene deserts result in viable mice. Nature 2004, 431:988-993.
    • (2004) Nature , vol.431 , pp. 988-993
    • Nóbrega, M.A.1    Zhu, Y.2    Plajzer-Frick, I.3
  • 186
    • 45449111373 scopus 로고    scopus 로고
    • Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites
    • Noyes M.B., Christensen R.G., Wakabayashi A., Stormo G.D., Brodsky M.H., Wolfe S.A. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell 2008, 133:1277-1289.
    • (2008) Cell , vol.133 , pp. 1277-1289
    • Noyes, M.B.1    Christensen, R.G.2    Wakabayashi, A.3    Stormo, G.D.4    Brodsky, M.H.5    Wolfe, S.A.6
  • 187
    • 17744380974 scopus 로고    scopus 로고
    • Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis
    • Oda-Ishii I., Bertrand V., Matsuo I., Lemaire P., Saiga H. Making very similar embryos with divergent genomes: conservation of regulatory mechanisms of Otx between the ascidians Halocynthia roretzi and Ciona intestinalis. Development (Cambridge, England) 2005, 132:1663-1674.
    • (2005) Development (Cambridge, England) , vol.132 , pp. 1663-1674
    • Oda-Ishii, I.1    Bertrand, V.2    Matsuo, I.3    Lemaire, P.4    Saiga, H.5
  • 189
    • 0032519586 scopus 로고    scopus 로고
    • Different core promoters possess distinct regulatory activities in the Drosophila embryo
    • Ohtsuki S., Levine M., Cai H.N. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev. 1998, 12:547-556.
    • (1998) Genes Dev. , vol.12 , pp. 547-556
    • Ohtsuki, S.1    Levine, M.2    Cai, H.N.3
  • 190
  • 191
    • 12744261452 scopus 로고    scopus 로고
    • Evolution and functional classification of vertebrate gene deserts
    • Ovcharenko I., Loots G.G., Nobrega M.A., et al. Evolution and functional classification of vertebrate gene deserts. Genome Res. 2005, 15:137-145.
    • (2005) Genome Res. , vol.15 , pp. 137-145
    • Ovcharenko, I.1    Loots, G.G.2    Nobrega, M.A.3
  • 192
    • 34250686675 scopus 로고    scopus 로고
    • Locating potential enhancer elements by comparative genomics using the EEL software
    • Palin K., Taipale J., Ukkonen E. Locating potential enhancer elements by comparative genomics using the EEL software. Nat. Protoc. 2006, 1:368-374.
    • (2006) Nat. Protoc. , vol.1 , pp. 368-374
    • Palin, K.1    Taipale, J.2    Ukkonen, E.3
  • 193
    • 34250017968 scopus 로고    scopus 로고
    • An atomic model of the interferon-beta enhanceosome
    • Panne D., Maniatis T., Harrison S.C. An atomic model of the interferon-beta enhanceosome. Cell 2007, 129:1111-1123.
    • (2007) Cell , vol.129 , pp. 1111-1123
    • Panne, D.1    Maniatis, T.2    Harrison, S.C.3
  • 194
    • 35548945031 scopus 로고    scopus 로고
    • Increased gamma-globin gene expression in beta-thalassemia intermedia patients correlates with a mutation in 3′hs1
    • Papachatzopoulou A., Kaimakis P., Pourfarzad F., et al. Increased gamma-globin gene expression in beta-thalassemia intermedia patients correlates with a mutation in 3′hs1. Am. J. Hematol. 2007, 82:1005-1009.
    • (2007) Am. J. Hematol. , vol.82 , pp. 1005-1009
    • Papachatzopoulou, A.1    Kaimakis, P.2    Pourfarzad, F.3
  • 195
    • 34249676873 scopus 로고    scopus 로고
    • ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors
    • Papatsenko D. ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors. Bioinformatics (Oxford, England) 2007, 23:1032-1034.
    • (2007) Bioinformatics (Oxford, England) , vol.23 , pp. 1032-1034
    • Papatsenko, D.1
  • 196
    • 23644436149 scopus 로고    scopus 로고
    • Computational identification of regulatory DNAs underlying animal development
    • Papatsenko D., Levine M. Computational identification of regulatory DNAs underlying animal development. Nat. Meth. 2005, 2:529-534.
    • (2005) Nat. Meth. , vol.2 , pp. 529-534
    • Papatsenko, D.1    Levine, M.2
  • 197
    • 33748705337 scopus 로고    scopus 로고
    • Conservation patterns in different functional sequence categories of divergent Drosophila species
    • Papatsenko D., Kislyuk A., Levine M., Dubchak I. Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics 2006, 88:431-442.
    • (2006) Genomics , vol.88 , pp. 431-442
    • Papatsenko, D.1    Kislyuk, A.2    Levine, M.3    Dubchak, I.4
  • 198
    • 70549090448 scopus 로고    scopus 로고
    • Organization of developmental enhancers in the Drosophila embryo
    • Papatsenko D., Goltsev Y., Levine M. Organization of developmental enhancers in the Drosophila embryo. Nucleic Acids Res. 2009, 37:5665-5677.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5665-5677
    • Papatsenko, D.1    Goltsev, Y.2    Levine, M.3
  • 199
    • 0034669066 scopus 로고    scopus 로고
    • Analysis of upstream elements in the huc promoter leads to the establishment of transgenic zebrafish with fluorescent neurons
    • Park H.C., Kim C.H., Bae Y.K., et al. Analysis of upstream elements in the huc promoter leads to the establishment of transgenic zebrafish with fluorescent neurons. Dev. Biol. 2000, 227:279-293.
    • (2000) Dev. Biol. , vol.227 , pp. 279-293
    • Park, H.C.1    Kim, C.H.2    Bae, Y.K.3
  • 200
    • 20144372906 scopus 로고    scopus 로고
    • Duplication of stat5-binding sites within the beta-lactoglobulin promoter compromises transcription in vivo
    • Pena R.N., Whitelaw C.B.A. Duplication of stat5-binding sites within the beta-lactoglobulin promoter compromises transcription in vivo. Biochimie 2005, 87:523-528.
    • (2005) Biochimie , vol.87 , pp. 523-528
    • Pena, R.N.1    Whitelaw, C.B.A.2
  • 201
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved non-coding sequences
    • Pennacchio L.A., Ahituv N., Moses A.M., et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 2006, 444:499-502.
    • (2006) Nature , vol.444 , pp. 499-502
    • Pennacchio, L.A.1    Ahituv, N.2    Moses, A.M.3
  • 202
    • 67549119096 scopus 로고    scopus 로고
    • CTCF: master weaver of the genome
    • Phillips J.E., Corces V.G. CTCF: master weaver of the genome. Cell 2009, 137:1194-1211.
    • (2009) Cell , vol.137 , pp. 1194-1211
    • Phillips, J.E.1    Corces, V.G.2
  • 203
    • 33751360783 scopus 로고    scopus 로고
    • Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA
    • Pierstorff N., Bergman C.M., Wiehe T. Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA. Bioinformatics 2006, 22:2858-2864.
    • (2006) Bioinformatics , vol.22 , pp. 2858-2864
    • Pierstorff, N.1    Bergman, C.M.2    Wiehe, T.3
  • 204
    • 0034647577 scopus 로고    scopus 로고
    • Chicken beta-globin 5′HS4 insulators function to reduce variability in transgenic founder mice
    • Potts W., Tucker D., Wood H., et al. Chicken beta-globin 5′HS4 insulators function to reduce variability in transgenic founder mice. Biochem. Biophys. Res. Commun. 2000, 273:1015-1018.
    • (2000) Biochem. Biophys. Res. Commun. , vol.273 , pp. 1015-1018
    • Potts, W.1    Tucker, D.2    Wood, H.3
  • 205
    • 18844376318 scopus 로고    scopus 로고
    • In vivo characterization of a vertebrate ultraconserved enhancer
    • Poulin F., Nobrega M.A., Plajzer-Frick I., et al. In vivo characterization of a vertebrate ultraconserved enhancer. Genomics 2005, 85:774-781.
    • (2005) Genomics , vol.85 , pp. 774-781
    • Poulin, F.1    Nobrega, M.A.2    Plajzer-Frick, I.3
  • 206
    • 33745628791 scopus 로고    scopus 로고
    • Close sequence comparisons are sufficient to identify human cis-regulatory elements
    • Prabhakar S., Poulin F., Shoukry M., et al. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res. 2006, 16:855-863.
    • (2006) Genome Res. , vol.16 , pp. 855-863
    • Prabhakar, S.1    Poulin, F.2    Shoukry, M.3
  • 207
    • 45749086679 scopus 로고    scopus 로고
    • The amphioxus genome and the evolution of the chordate karyotype
    • Putnam N.H., Butts T., Ferrier D.E.K., et al. The amphioxus genome and the evolution of the chordate karyotype. Nature 2008, 453:1064-1071.
    • (2008) Nature , vol.453 , pp. 1064-1071
    • Putnam, N.H.1    Butts, T.2    Ferrier, D.E.K.3
  • 208
    • 55549103719 scopus 로고    scopus 로고
    • E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites
    • Rabinovich A., Jin V.X., Rabinovich R., et al. E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res. 2008, 18:1763-1777.
    • (2008) Genome Res. , vol.18 , pp. 1763-1777
    • Rabinovich, A.1    Jin, V.X.2    Rabinovich, R.3
  • 209
    • 55049105999 scopus 로고    scopus 로고
    • Disruption of an AP-2alpha binding site in an Irf6 enhancer is associated with cleft lip
    • Rahimov F., Marazita M.L., Visel A., et al. Disruption of an AP-2alpha binding site in an Irf6 enhancer is associated with cleft lip. Nat. Genet. 2008, 40:1341-1347.
    • (2008) Nat. Genet. , vol.40 , pp. 1341-1347
    • Rahimov, F.1    Marazita, M.L.2    Visel, A.3
  • 210
    • 2942576308 scopus 로고    scopus 로고
    • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
    • 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 Bioinform. 2002, 3:30.
    • (2002) BMC Bioinform. , vol.3 , pp. 30
    • Rajewsky, N.1    Vergassola, M.2    Gaul, U.3    Siggia, E.D.4
  • 211
    • 0037162497 scopus 로고    scopus 로고
    • Score: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. site clustering over random expectation
    • Rebeiz M., Reeves N.L., Posakony J.W. Score: a computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. site clustering over random expectation. Proc. Natl Acad. Sci. USA 2002, 99:9888-9893.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 9888-9893
    • Rebeiz, M.1    Reeves, N.L.2    Posakony, J.W.3
  • 212
    • 38349153236 scopus 로고    scopus 로고
    • Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time
    • Retelska D., Beaudoing E., Notredame C., et al. Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time. BMC Genomics 2007, 8:398.
    • (2007) BMC Genomics , vol.8 , pp. 398
    • Retelska, D.1    Beaudoing, E.2    Notredame, C.3
  • 213
    • 34250729138 scopus 로고    scopus 로고
    • Functional demarcation of active and silent chromatin domains in human hox loci by noncoding RNAs
    • Rinn J.L., Kertesz M., Wang J.K., et al. Functional demarcation of active and silent chromatin domains in human hox loci by noncoding RNAs. Cell 2007, 129:1311-1323.
    • (2007) Cell , vol.129 , pp. 1311-1323
    • Rinn, J.L.1    Kertesz, M.2    Wang, J.K.3
  • 215
    • 33846700587 scopus 로고    scopus 로고
    • Predicting transcription factor affinities to DNA from a biophysical model
    • Roider H.G., Kanhere A., Manke T., et al. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics 2007, 23:134-141.
    • (2007) Bioinformatics , vol.23 , pp. 134-141
    • Roider, H.G.1    Kanhere, A.2    Manke, T.3
  • 216
    • 0041677607 scopus 로고    scopus 로고
    • Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation
    • Romano L.A., Wray G.A. Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation. Development 2003, 130:4187-4199.
    • (2003) Development , vol.130 , pp. 4187-4199
    • Romano, L.A.1    Wray, G.A.2
  • 217
    • 10644234650 scopus 로고    scopus 로고
    • Visualization of trans-homolog enhancer-promoter interactions at the abd-b hox locus in the Drosophila embryo
    • Ronshaugen M., Levine M. Visualization of trans-homolog enhancer-promoter interactions at the abd-b hox locus in the Drosophila embryo. Dev. Cell 2004, 7:925-932.
    • (2004) Dev. Cell , vol.7 , pp. 925-932
    • Ronshaugen, M.1    Levine, M.2
  • 218
    • 33846617772 scopus 로고    scopus 로고
    • Long-range conserved non-coding SHOX sequences regulate expression in developing chicken limb and are associated with short stature phenotypes in human patients
    • Sabherwal N., Bangs F., Röth R., et al. Long-range conserved non-coding SHOX sequences regulate expression in developing chicken limb and are associated with short stature phenotypes in human patients. Hum. Mol. Genet. 2007, 16:210-222.
    • (2007) Hum. Mol. Genet. , vol.16 , pp. 210-222
    • Sabherwal, N.1    Bangs, F.2    Röth, R.3
  • 219
    • 58149311049 scopus 로고    scopus 로고
    • Identification and characterization of new long conserved noncoding sequences in vertebrates
    • Sakuraba Y., Kimura T., Masuya H., et al. Identification and characterization of new long conserved noncoding sequences in vertebrates. Mamm. Genome 2008, 19:703-712.
    • (2008) Mamm. Genome , vol.19 , pp. 703-712
    • Sakuraba, Y.1    Kimura, T.2    Masuya, H.3
  • 220
    • 33644514069 scopus 로고    scopus 로고
    • Noncoding RNAs of trithorax response elements recruit Drosophila ash1 to ultrabithorax
    • Sanchez-Elsner T., Gou D., Kremmer E., et al. Noncoding RNAs of trithorax response elements recruit Drosophila ash1 to ultrabithorax. Science 2006, 311:1118-1123.
    • (2006) Science , vol.311 , pp. 1118-1123
    • Sanchez-Elsner, T.1    Gou, D.2    Kremmer, E.3
  • 221
    • 22144473057 scopus 로고    scopus 로고
    • Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes
    • Sandelin A., Bailey P., Bruce S., et al. Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes. BMC Genomics 2004, 5:99.
    • (2004) BMC Genomics , vol.5 , pp. 99
    • Sandelin, A.1    Bailey, P.2    Bruce, S.3
  • 222
    • 34247579156 scopus 로고    scopus 로고
    • A survey of motif discovery methods in an integrated framework
    • Sandve G.K., Drabløs F. A survey of motif discovery methods in an integrated framework. Biol. Direct 2006, 1:11.
    • (2006) Biol. Direct , vol.1 , pp. 11
    • Sandve, G.K.1    Drabløs, F.2
  • 223
    • 0141790017 scopus 로고    scopus 로고
    • Identification of cis-regulatory elements in the mouse Pax9/nkx2-9 genomic region: implication for evolutionary conserved synteny
    • Santagati F., Abe K., Schmidt V., et al. Identification of cis-regulatory elements in the mouse Pax9/nkx2-9 genomic region: implication for evolutionary conserved synteny. Genetics 2003, 165:235-242.
    • (2003) Genetics , vol.165 , pp. 235-242
    • Santagati, F.1    Abe, K.2    Schmidt, V.3
  • 224
    • 77952908743 scopus 로고    scopus 로고
    • A large fraction of extragenic RNA pol II transcription sites overlap enhancers
    • De Santa F., Barozzi I., Mietton F., et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 2010, 8:e1000384.
    • (2010) PLoS Biol. , vol.8
    • De Santa, F.1    Barozzi, I.2    Mietton, F.3
  • 225
    • 43349091196 scopus 로고    scopus 로고
    • Combining statistical alignment and phylogenetic footprinting to detect regulatory elements
    • Satija R., Pachter L., Hein J. Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics 2008, 24:1236-1242.
    • (2008) Bioinformatics , vol.24 , pp. 1236-1242
    • Satija, R.1    Pachter, L.2    Hein, J.3
  • 227
    • 19344375742 scopus 로고    scopus 로고
    • Transcriptional control in the segmentation gene network of Drosophila
    • Schroeder M.D., Pearce M., Fak J., et al. Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol. 2004, 2:E271.
    • (2004) PLoS Biol. , vol.2
    • Schroeder, M.D.1    Pearce, M.2    Fak, J.3
  • 228
    • 38749127589 scopus 로고    scopus 로고
    • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    • Segal E., Raveh-Sadka T., Schroeder M., et al. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 2008, 451:535-540.
    • (2008) Nature , vol.451 , pp. 535-540
    • Segal, E.1    Raveh-Sadka, T.2    Schroeder, M.3
  • 229
    • 59849119654 scopus 로고    scopus 로고
    • Recombineering: a homologous recombination-based method of genetic engineering
    • Sharan S.K., Thomason L.C., Kuznetsov S.G., et al. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 2009, 4:206-223.
    • (2009) Nat. Protoc. , vol.4 , pp. 206-223
    • Sharan, S.K.1    Thomason, L.C.2    Kuznetsov, S.G.3
  • 231
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel A., Bejerano G., Pedersen J.S., et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005, 15:1034-1050.
    • (2005) Genome Res. , vol.15 , pp. 1034-1050
    • Siepel, A.1    Bejerano, G.2    Pedersen, J.S.3
  • 232
    • 33644873674 scopus 로고    scopus 로고
    • Dbtgr: a database of tunicate promoters and their regulatory elements
    • Sierro N., Kusakabe T., Park K., et al. Dbtgr: a database of tunicate promoters and their regulatory elements. Nucleic Acids Res. 2006, 34:D552-D555.
    • (2006) Nucleic Acids Res. , vol.34
    • Sierro, N.1    Kusakabe, T.2    Park, K.3
  • 233
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4c)
    • Simonis M., Klous P., Splinter E., et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4c). Nat. Genet. 2006, 38:1348-1354.
    • (2006) Nat. Genet. , vol.38 , pp. 1348-1354
    • Simonis, M.1    Klous, P.2    Splinter, E.3
  • 234
    • 16344388566 scopus 로고    scopus 로고
    • Sequence turnover and tandem repeats in cis-regulatory modules in Drosophila
    • Sinha S., Siggia E.D. Sequence turnover and tandem repeats in cis-regulatory modules in Drosophila. Mol. Biol. Evol. 2005, 22:874-885.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 874-885
    • Sinha, S.1    Siggia, E.D.2
  • 235
    • 0035477896 scopus 로고    scopus 로고
    • Core promoters: active contributors to combinatorial gene regulation
    • Smale S.T. Core promoters: active contributors to combinatorial gene regulation. Genes Dev. 2001, 15:2503-2508.
    • (2001) Genes Dev. , vol.15 , pp. 2503-2508
    • Smale, S.T.1
  • 236
    • 33846515642 scopus 로고    scopus 로고
    • Tissue-specific regulatory elements in mammalian promoters
    • Smith A.D., Sumazin P., Zhang M.Q. Tissue-specific regulatory elements in mammalian promoters. Mol. Syst. Biol. 2007, 3:73.
    • (2007) Mol. Syst. Biol. , vol.3 , pp. 73
    • Smith, A.D.1    Sumazin, P.2    Zhang, M.Q.3
  • 237
    • 42049091628 scopus 로고    scopus 로고
    • A protocol describing the principles of cis-regulatory analysis in the sea urchin
    • Smith J. A protocol describing the principles of cis-regulatory analysis in the sea urchin. Nat. Protoc. 2008, 3:710-718.
    • (2008) Nat. Protoc. , vol.3 , pp. 710-718
    • Smith, J.1
  • 238
    • 66749180667 scopus 로고    scopus 로고
    • Epigenetic temporal control of mouse Hox genes in vivo
    • Soshnikova N., Duboule D. Epigenetic temporal control of mouse Hox genes in vivo. Science 2009, 324:1320-1323.
    • (2009) Science , vol.324 , pp. 1320-1323
    • Soshnikova, N.1    Duboule, D.2
  • 239
    • 39049130281 scopus 로고    scopus 로고
    • Global control regions and regulatory landscapes in vertebrate development and evolution
    • Spitz F., Duboule D. Global control regions and regulatory landscapes in vertebrate development and evolution. Adv. Genet. 2008, 61:175-205.
    • (2008) Adv. Genet. , vol.61 , pp. 175-205
    • Spitz, F.1    Duboule, D.2
  • 240
    • 0038613098 scopus 로고    scopus 로고
    • A global control region defines a chromosomal regulatory landscape containing the HoxD cluster
    • Spitz F., Gonzalez F., Duboule D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 2003, 113:405-417.
    • (2003) Cell , vol.113 , pp. 405-417
    • Spitz, F.1    Gonzalez, F.2    Duboule, D.3
  • 241
    • 0020554565 scopus 로고
    • The effect of chromosomal position on the expression of the Drosophila xanthine dehydrogenase gene
    • Spradling A.C., Rubin G.M. The effect of chromosomal position on the expression of the Drosophila xanthine dehydrogenase gene. Cell 1983, 34:47-57.
    • (1983) Cell , vol.34 , pp. 47-57
    • Spradling, A.C.1    Rubin, G.M.2
  • 242
    • 38949097100 scopus 로고    scopus 로고
    • Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock
    • Stephen S., Pheasant M., Makunin I.V., et al. Large-scale appearance of ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. Mol. Biol. Evol. 2008, 25:402-408.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 402-408
    • Stephen, S.1    Pheasant, M.2    Makunin, I.V.3
  • 243
    • 33749000852 scopus 로고    scopus 로고
    • Conserved distances between vertebrate highly conserved elements
    • Sun H., Skogerbø G., Chen R. Conserved distances between vertebrate highly conserved elements. Hum. Mol. Genet. 2006, 15:2911-2922.
    • (2006) Hum. Mol. Genet. , vol.15 , pp. 2911-2922
    • Sun, H.1    Skogerbø, G.2    Chen, R.3
  • 244
    • 58149186547 scopus 로고    scopus 로고
    • A novel conserved Evx1 enhancer links spinal interneuron morphology and cis-regulation from fish to mammals
    • Suster M.L., Kania A., Liao M., et al. A novel conserved Evx1 enhancer links spinal interneuron morphology and cis-regulation from fish to mammals. Dev. Biol. 2009, 325:422-433.
    • (2009) Dev. Biol. , vol.325 , pp. 422-433
    • Suster, M.L.1    Kania, A.2    Liao, M.3
  • 245
    • 0036081146 scopus 로고    scopus 로고
    • DBTSS: database of human transcriptional start sites and full-length cDNAs
    • Suzuki Y., Yamashita R., Nakai K., et al. DBTSS: database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 2002, 30:328-331.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 328-331
    • Suzuki, Y.1    Yamashita, R.2    Nakai, K.3
  • 246
    • 61449212191 scopus 로고    scopus 로고
    • Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
    • Taher L., Ovcharenko I. Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics 2009, 25:578-584.
    • (2009) Bioinformatics , vol.25 , pp. 578-584
    • Taher, L.1    Ovcharenko, I.2
  • 247
    • 32944478048 scopus 로고    scopus 로고
    • A quantitative approach to the study of cell shapes and interactions during early chordate embryogenesis
    • Tassy O., Daian F., Hudson C., et al. A quantitative approach to the study of cell shapes and interactions during early chordate embryogenesis. Curr. Biol. 2006, 16:345-358.
    • (2006) Curr. Biol. , vol.16 , pp. 345-358
    • Tassy, O.1    Daian, F.2    Hudson, C.3
  • 248
    • 33845303175 scopus 로고    scopus 로고
    • ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements
    • Taylor J., Tyekucheva S., King D.C., et al. ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 2006, 16:1596-1604.
    • (2006) Genome Res. , vol.16 , pp. 1596-1604
    • Taylor, J.1    Tyekucheva, S.2    King, D.C.3
  • 249
    • 0029617947 scopus 로고
    • Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome
    • Thanos D., Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 1995, 83:1091-1100.
    • (1995) Cell , vol.83 , pp. 1091-1100
    • Thanos, D.1    Maniatis, T.2
  • 250
    • 21144439147 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of transcription factor binding sites
    • Tompa M., Li N., Bailey T.L., et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol. 2005, 23:137-144.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 137-144
    • Tompa, M.1    Li, N.2    Bailey, T.L.3
  • 251
    • 0031581855 scopus 로고    scopus 로고
    • Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome
    • Tronche F., Ringeisen F., Blumenfeld M., et al. Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol. 1997, 266:231-245.
    • (1997) J. Mol. Biol. , vol.266 , pp. 231-245
    • Tronche, F.1    Ringeisen, F.2    Blumenfeld, M.3
  • 252
    • 68549104043 scopus 로고    scopus 로고
    • An evolutionarily conserved nested gene pair- mab21 and lrba/nbea in metazoan
    • Tsang W.H., Shek K.F., Lee T.Y., et al. An evolutionarily conserved nested gene pair- mab21 and lrba/nbea in metazoan. Genomics 2009.
    • (2009) Genomics
    • Tsang, W.H.1    Shek, K.F.2    Lee, T.Y.3
  • 253
    • 58149512003 scopus 로고    scopus 로고
    • A regulatory module embedded in the coding region of hoxa2 controls expression in rhombomere 2
    • Tümpel S., Cambronero F., Sims C., et al. A regulatory module embedded in the coding region of hoxa2 controls expression in rhombomere 2. Proc. Natl. Acad. Sci. USA 2008, 105:20077-20082.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 20077-20082
    • Tümpel, S.1    Cambronero, F.2    Sims, C.3
  • 254
    • 61849087365 scopus 로고    scopus 로고
    • A toolkit and robust pipeline for the generation of fosmid-based reporter genes in c. elegans
    • Tursun B., Cochella L., Carrera I., et al. A toolkit and robust pipeline for the generation of fosmid-based reporter genes in c. elegans. PLoS ONE 2009, 4:e4625.
    • (2009) PLoS ONE , vol.4
    • Tursun, B.1    Cochella, L.2    Carrera, I.3
  • 255
    • 0037389626 scopus 로고    scopus 로고
    • Functional analysis of chicken sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals
    • Uchikawa M., Ishida Y., Takemoto T., et al. Functional analysis of chicken sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals. Dev. Cell 2003, 4:509-519.
    • (2003) Dev. Cell , vol.4 , pp. 509-519
    • Uchikawa, M.1    Ishida, Y.2    Takemoto, T.3
  • 256
    • 13244272059 scopus 로고    scopus 로고
    • Proximity among distant regulatory elements at the beta-globin locus requires gata-1 and fog-1
    • Vakoc C.R., Letting D.L., Gheldof N., et al. Proximity among distant regulatory elements at the beta-globin locus requires gata-1 and fog-1. Mol. Cell 2005, 17:453-462.
    • (2005) Mol. Cell , vol.17 , pp. 453-462
    • Vakoc, C.R.1    Letting, D.L.2    Gheldof, N.3
  • 257
    • 75649084887 scopus 로고    scopus 로고
    • Modeling tissue-specific structural patterns in human and mouse promoters
    • Vandenbon A., Nakai K. Modeling tissue-specific structural patterns in human and mouse promoters. Nucleic Acids Res. 2010, 38:17-25.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 17-25
    • Vandenbon, A.1    Nakai, K.2
  • 258
    • 22144459722 scopus 로고    scopus 로고
    • Prediction of cis-regulatory elements using binding site matrices-the successes, the failures and the reasons for both
    • Vavouri T., Elgar G. Prediction of cis-regulatory elements using binding site matrices-the successes, the failures and the reasons for both. Curr. Opin. Genet. Dev. 2005, 15:395-402.
    • (2005) Curr. Opin. Genet. Dev. , vol.15 , pp. 395-402
    • Vavouri, T.1    Elgar, G.2
  • 259
    • 29444452159 scopus 로고    scopus 로고
    • Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key
    • Vavouri T., McEwen G.K., Woolfe A., et al. Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key. Trends Genet. 2006, 22:5-10.
    • (2006) Trends Genet. , vol.22 , pp. 5-10
    • Vavouri, T.1    McEwen, G.K.2    Woolfe, A.3
  • 260
    • 34447500684 scopus 로고    scopus 로고
    • Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans
    • Vavouri T., Walter K., Gilks W.R., et al. Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol. 2007, 8:R15.
    • (2007) Genome Biol. , vol.8
    • Vavouri, T.1    Walter, K.2    Gilks, W.R.3
  • 261
    • 67349098844 scopus 로고    scopus 로고
    • Versatile p[acman] bac libraries for transgenesis studies in drosophila melanogaster
    • Venken K.J.T., Carlson J.W., Schulze K.L., et al. Versatile p[acman] bac libraries for transgenesis studies in drosophila melanogaster. Nat. Methods 2009, 6:431-434.
    • (2009) Nat. Methods , vol.6 , pp. 431-434
    • Venken, K.J.T.1    Carlson, J.W.2    Schulze, K.L.3
  • 262
    • 67349255443 scopus 로고    scopus 로고
    • Functional autonomy of distant-acting human enhancers
    • Visel A., Akiyama J.A., Shoukry M., et al. Functional autonomy of distant-acting human enhancers. Genomics 2009, 93:509-513.
    • (2009) Genomics , vol.93 , pp. 509-513
    • Visel, A.1    Akiyama, J.A.2    Shoukry, M.3
  • 263
    • 60149091656 scopus 로고    scopus 로고
    • ChIP-seq accurately predicts tissue-specific activity of enhancers
    • Visel A., Blow M.J., Li Z., et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009, 457:854-858.
    • (2009) Nature , vol.457 , pp. 854-858
    • Visel, A.1    Blow, M.J.2    Li, Z.3
  • 265
    • 65249118705 scopus 로고    scopus 로고
    • Co-regulated expression of Hand2 and Dein by a bidirectional promoter with asymmetrical activity in neuroblastoma
    • Voth H., Oberthuer A., Simon T., et al. Co-regulated expression of Hand2 and Dein by a bidirectional promoter with asymmetrical activity in neuroblastoma. BMC Mol. Biol. 2009, 10:28.
    • (2009) BMC Mol. Biol. , vol.10 , pp. 28
    • Voth, H.1    Oberthuer, A.2    Simon, T.3
  • 266
    • 38549094621 scopus 로고    scopus 로고
    • DBTSS: database of transcription start sites, progress report 2008
    • Wakaguri H., Yamashita R., Suzuki Y., et al. DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res. 2008, 36:D97-D101.
    • (2008) Nucleic Acids Res. , vol.36
    • Wakaguri, H.1    Yamashita, R.2    Suzuki, Y.3
  • 267
    • 22144494134 scopus 로고    scopus 로고
    • Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences
    • Walter K., Abnizova I., Elgar G., et al. Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences. Trends Genet. 2005, 21:436-440.
    • (2005) Trends Genet. , vol.21 , pp. 436-440
    • Walter, K.1    Abnizova, I.2    Elgar, G.3
  • 268
    • 33845316442 scopus 로고    scopus 로고
    • Experimental validation of predicted mammalian erythroid cis-regulatory modules
    • Wang H., Zhang Y., Cheng Y., et al. Experimental validation of predicted mammalian erythroid cis-regulatory modules. Genome Res. 2006, 16:1480-1492.
    • (2006) Genome Res. , vol.16 , pp. 1480-1492
    • Wang, H.1    Zhang, Y.2    Cheng, Y.3
  • 269
    • 34147170895 scopus 로고    scopus 로고
    • Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons
    • Wang Q., Prabhakar S., Chanan S., et al. Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol. 2007, 8:R1.
    • (2007) Genome Biol. , vol.8
    • Wang, Q.1    Prabhakar, S.2    Chanan, S.3
  • 270
    • 0036071731 scopus 로고    scopus 로고
    • Functional analysis of the proximal promoter regions of fish Rhodopsin and MYF-5 genes using transgenesis
    • Wang T., Chen Y., Liu C., et al. Functional analysis of the proximal promoter regions of fish Rhodopsin and MYF-5 genes using transgenesis. Mar. Biotechnol. 2002, 4:247-255.
    • (2002) Mar. Biotechnol. , vol.4 , pp. 247-255
    • Wang, T.1    Chen, Y.2    Liu, C.3
  • 271
    • 33847662814 scopus 로고    scopus 로고
    • Comparison of Pax1/9 locus reveals 500-myr-old syntenic block and evolutionary conserved noncoding regions
    • Wang W., Zhong J., Su B., et al. Comparison of Pax1/9 locus reveals 500-myr-old syntenic block and evolutionary conserved noncoding regions. Mol. Biol. Evol. 2007, 24:784-791.
    • (2007) Mol. Biol. Evol. , vol.24 , pp. 784-791
    • Wang, W.1    Zhong, J.2    Su, B.3
  • 272
    • 34250331200 scopus 로고    scopus 로고
    • Structured RNAs in the ENCODE selected regions of the human genome
    • Washietl S., Pedersen J.S., Korbel J.O., et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007, 17:852-864.
    • (2007) Genome Res. , vol.17 , pp. 852-864
    • Washietl, S.1    Pedersen, J.S.2    Korbel, J.O.3
  • 273
    • 0032562789 scopus 로고    scopus 로고
    • Identification of regulatory regions which confer muscle-specific gene expression
    • Wasserman W.W., Fickett J.W. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 1998, 278:167-181.
    • (1998) J. Mol. Biol. , vol.278 , pp. 167-181
    • Wasserman, W.W.1    Fickett, J.W.2
  • 274
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • Wasserman W.W., Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 2004, 5:276-287.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 275
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Waterston R.H., Lindblad-Toh K., Birney E., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
    • (2002) Nature , vol.420 , pp. 520-562
    • Waterston, R.H.1    Lindblad-Toh, K.2    Birney, E.3
  • 276
    • 49249110970 scopus 로고    scopus 로고
    • Global analysis of in vivo foxa2-binding sites in mouse adult liver using massively parallel sequencing
    • Wederell E.D., Bilenky M., Cullum R., et al. Global analysis of in vivo foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res. 2008, 36:4549-4564.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 4549-4564
    • Wederell, E.D.1    Bilenky, M.2    Cullum, R.3
  • 277
    • 2942596447 scopus 로고    scopus 로고
    • Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in c. elegans
    • Wenick A.S., Hobert O. Genomic cis-regulatory architecture and trans-acting regulators of a single interneuron-specific gene battery in c. elegans. Dev. Cell 2004, 6:757-770.
    • (2004) Dev. Cell , vol.6 , pp. 757-770
    • Wenick, A.S.1    Hobert, O.2
  • 278
    • 36148967738 scopus 로고    scopus 로고
    • Multiple conserved regulatory elements with overlapping functions determine Sox10 expression in mouse embryogenesis
    • Werner T., Hammer A., Wahlbuhl M., Bösl M.R., Wegner M. Multiple conserved regulatory elements with overlapping functions determine Sox10 expression in mouse embryogenesis. Nucleic Acids Res. 2007, 35:6526-6538.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 6526-6538
    • Werner, T.1    Hammer, A.2    Wahlbuhl, M.3    Bösl, M.R.4    Wegner, M.5
  • 279
    • 17444369067 scopus 로고    scopus 로고
    • Remote control of gene transcription
    • West A.G., Fraser P. Remote control of gene transcription. Hum. Mol. Genet. 2005, 14(Spec. No. 1):R101-R111.
    • (2005) Hum. Mol. Genet. , vol.14 , Issue.SPEC. NO. 1
    • West, A.G.1    Fraser, P.2
  • 280
    • 66749176636 scopus 로고    scopus 로고
    • Conserved elements within open reading frames of mammalian HOX genes
    • Woltering J.M., Duboule D. Conserved elements within open reading frames of mammalian HOX genes. J. Biol. 2009, 8:17.
    • (2009) J. Biol. , vol.8 , pp. 17
    • Woltering, J.M.1    Duboule, D.2
  • 281
    • 34548527597 scopus 로고    scopus 로고
    • Comparative genomics using fugu reveals insights into regulatory subfunctionalization
    • Woolfe A., Elgar G. Comparative genomics using fugu reveals insights into regulatory subfunctionalization. Genome Biol. 2007, 8:R53.
    • (2007) Genome Biol. , vol.8
    • Woolfe, A.1    Elgar, G.2
  • 282
    • 39049141215 scopus 로고    scopus 로고
    • Organization of conserved elements near key developmental regulators in vertebrate genomes
    • Woolfe A., Elgar G. Organization of conserved elements near key developmental regulators in vertebrate genomes. Adv. Genet. 2008, 61:307-338.
    • (2008) Adv. Genet. , vol.61 , pp. 307-338
    • Woolfe, A.1    Elgar, G.2
  • 283
    • 20044366725 scopus 로고    scopus 로고
    • Highly conserved non-coding sequences are associated with vertebrate development
    • Woolfe A., Goodson M., Goode D.K., et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 2005, 3:e7.
    • (2005) PLoS Biol. , vol.3
    • Woolfe, A.1    Goodson, M.2    Goode, D.K.3
  • 284
    • 33645028299 scopus 로고    scopus 로고
    • Evolutionary and functional analysis of the tailless enhancer in musca domestica and Drosophila melanogaster
    • Wratten N.S., McGregor A.P., Shaw P.J., et al. Evolutionary and functional analysis of the tailless enhancer in musca domestica and Drosophila melanogaster. Evol. Dev. 2006, 8:6-15.
    • (2006) Evol. Dev. , vol.8 , pp. 6-15
    • Wratten, N.S.1    McGregor, A.P.2    Shaw, P.J.3
  • 285
    • 33746801653 scopus 로고    scopus 로고
    • A family of conserved noncoding elements derived from an ancient transposable element
    • Xie X., Kamal M., Lander E.S. A family of conserved noncoding elements derived from an ancient transposable element. Proc. Natl. Acad. Sci. USA 2006, 103:11659-11664.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 11659-11664
    • Xie, X.1    Kamal, M.2    Lander, E.S.3
  • 286
    • 61849084830 scopus 로고    scopus 로고
    • Meis1 intronic risk haplotype associated with restless legs syndrome affects its mRNA and protein expression levels
    • Xiong L., Catoire H., Dion P., et al. Meis1 intronic risk haplotype associated with restless legs syndrome affects its mRNA and protein expression levels. Hum. Mol. Genet. 2009, 18:1065-1074.
    • (2009) Hum. Mol. Genet. , vol.18 , pp. 1065-1074
    • Xiong, L.1    Catoire, H.2    Dion, P.3
  • 287
    • 0036196877 scopus 로고    scopus 로고
    • Redundant and unique roles of two enhancer elements in the Tcrgamma locus in gene regulation and Gammadelta T cell development
    • Xiong N., Kang C., Raulet D.H. Redundant and unique roles of two enhancer elements in the Tcrgamma locus in gene regulation and Gammadelta T cell development. Immunity 2002, 16:453-463.
    • (2002) Immunity , vol.16 , pp. 453-463
    • Xiong, N.1    Kang, C.2    Raulet, D.H.3
  • 288
    • 35949000033 scopus 로고    scopus 로고
    • A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members
    • Xu X., Bieda M., Jin V.X., Rabinovich A., Oberley M.J., Green R., Farnham P.J. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res. 2007, 17:1550-1561.
    • (2007) Genome Res. , vol.17 , pp. 1550-1561
    • Xu, X.1    Bieda, M.2    Jin, V.X.3    Rabinovich, A.4    Oberley, M.J.5    Green, R.6    Farnham, P.J.7
  • 289
    • 33746512547 scopus 로고    scopus 로고
    • Shared long-range regulatory elements coordinate expression of a gene cluster encoding nicotinic receptor heteromeric subtypes
    • Xu X., Scott M.M., Deneris E.S. Shared long-range regulatory elements coordinate expression of a gene cluster encoding nicotinic receptor heteromeric subtypes. Mol. Cell. Biol. 2006, 26:5636-5649.
    • (2006) Mol. Cell. Biol. , vol.26 , pp. 5636-5649
    • Xu, X.1    Scott, M.M.2    Deneris, E.S.3
  • 290
    • 0037349438 scopus 로고    scopus 로고
    • Targeted deletion of a branchial arch-specific enhancer reveals a role of Dhand in craniofacial development
    • Yanagisawa H., Clouthier D.E., Richardson J.A., et al. Targeted deletion of a branchial arch-specific enhancer reveals a role of Dhand in craniofacial development. Development 2003, 130:1069-1078.
    • (2003) Development , vol.130 , pp. 1069-1078
    • Yanagisawa, H.1    Clouthier, D.E.2    Richardson, J.A.3
  • 291
    • 59849088379 scopus 로고    scopus 로고
    • Next generation tools for high-throughput promoter and expression analysis employing single-copy knock-ins at the HPRT1 locus
    • Yang G.S., Banks K.G., Bonaguro R.J., et al. Next generation tools for high-throughput promoter and expression analysis employing single-copy knock-ins at the HPRT1 locus. Genomics 2009, 93:196-204.
    • (2009) Genomics , vol.93 , pp. 196-204
    • Yang, G.S.1    Banks, K.G.2    Bonaguro, R.J.3
  • 292
    • 34447525515 scopus 로고    scopus 로고
    • Transgenic analysis of the anterior eye-specific enhancers of the zebrafish Gelsolin-like 1 (gsnl1) gene
    • Yoshikawa S., Norcom E., Nakamura H., et al. Transgenic analysis of the anterior eye-specific enhancers of the zebrafish Gelsolin-like 1 (gsnl1) gene. Dev. Dyn. 2007, 236:1929-1938.
    • (2007) Dev. Dyn. , vol.236 , pp. 1929-1938
    • Yoshikawa, S.1    Norcom, E.2    Nakamura, H.3
  • 293
    • 36949030484 scopus 로고    scopus 로고
    • Predicting gene expression from sequence: a reexamination
    • Yuan Y., Guo L., Shen L., et al. Predicting gene expression from sequence: a reexamination. PLoS Comput. Biol. 2007, 3:e243.
    • (2007) PLoS Comput. Biol. , vol.3
    • Yuan, Y.1    Guo, L.2    Shen, L.3
  • 294
    • 0032549745 scopus 로고    scopus 로고
    • Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene
    • Yuh C.H., Bolouri H., Davidson E.H. Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene. Science 1998, 279:1896-1902.
    • (1998) Science , vol.279 , pp. 1896-1902
    • Yuh, C.H.1    Bolouri, H.2    Davidson, E.H.3
  • 295
    • 33646844116 scopus 로고    scopus 로고
    • A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome
    • Zhang C., Xuan Z., Otto S., et al. A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Res. 2006, 34:2238-2246.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2238-2246
    • Zhang, C.1    Xuan, Z.2    Otto, S.3
  • 296
    • 34250366235 scopus 로고    scopus 로고
    • Statistical analysis of the genomic distribution and correlation of regulatory elements in the encode regions
    • Zhang Z.D., Paccanaro A., Fu Y., et al. Statistical analysis of the genomic distribution and correlation of regulatory elements in the encode regions. Genome Res. 2007, 17:787-797.
    • (2007) Genome Res. , vol.17 , pp. 787-797
    • Zhang, Z.D.1    Paccanaro, A.2    Fu, Y.3
  • 297
    • 0035477239 scopus 로고    scopus 로고
    • Activation of the human PAX6 gene through the exon 1 enhancer by transcription factors SEF and Sp1
    • Zheng J.B., Zhou Y.H., Maity T., et al. Activation of the human PAX6 gene through the exon 1 enhancer by transcription factors SEF and Sp1. Nucleic Acids Res. 2001, 29:4070-4078.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 4070-4078
    • Zheng, J.B.1    Zhou, Y.H.2    Maity, T.3
  • 298
    • 70449132583 scopus 로고    scopus 로고
    • Combinatorial binding predicts spatio-temporal cis-regulatory activity
    • [NCICRF]
    • Zinzen R.P., Girardot C., Gagneur J., Braun M., Furlong E.E.M. Combinatorial binding predicts spatio-temporal cis-regulatory activity. Nature 2009, 462:65-70. [NCICRF]. http://recombineering.ncifcrf.gov.
    • (2009) Nature , vol.462 , pp. 65-70
    • Zinzen, R.P.1    Girardot, C.2    Gagneur, J.3    Braun, M.4    Furlong, E.E.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.