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Volumn 17, Issue 6, 2007, Pages 898-909

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; STAT1 PROTEIN; TRANSCRIPTION FACTOR;

EID: 34250332235     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5583007     Document Type: Article
Times cited : (173)

References (41)
  • 1
  • 5
    • 0034981517 scopus 로고    scopus 로고
    • STAT proteins: Signal transducers and activators of transcription
    • Bromberg, J. and Chen, X. 2001. STAT proteins: Signal transducers and activators of transcription. Methods Enzymol. 333: 138-151.
    • (2001) Methods Enzymol , vol.333 , pp. 138-151
    • Bromberg, J.1    Chen, X.2
  • 6
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck, M.J. and Lieb, J.D. 2004. ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83: 349-360.
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 7
    • 10744226888 scopus 로고    scopus 로고
    • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    • Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J., et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1    Bekiranov, S.2    Ng, H.H.3    Kapranov, P.4    Sekinger, E.A.5    Kampa, D.6    Piccolboni, A.7    Sementchenko, V.8    Cheng, J.9    Williams, A.J.10
  • 8
    • 16344393332 scopus 로고    scopus 로고
    • Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements
    • Chen, J. and Sadowski, I. 2005. Identification of the mismatch repair genes PMS2 and MLH1 as p53 target genes by using serial analysis of binding elements. Proc. Natl. Acad. Sci. 102: 4813-4818.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 4813-4818
    • Chen, J.1    Sadowski, I.2
  • 10
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia Of DNA Elements) Project
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
    • (2004) Science , vol.306 , pp. 636-640
  • 11
    • 34250305146 scopus 로고    scopus 로고
    • Indentification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • The ENCODE Project Consortium, in press
    • The ENCODE Project Consortium. 2007. Indentification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (in press).
    • (2007) Nature
  • 13
    • 29144475515 scopus 로고    scopus 로고
    • Global changes in STAT target selection and transcription regulation upon interferon treatments
    • Hartman, S.E., Bertone, P., Nath, A.K., Royce, T.E., Gerstein, M., Weissman, S., and Snyder, M. 2005. Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes & Dev. 19: 2953-2968.
    • (2005) Genes & Dev , vol.19 , pp. 2953-2968
    • Hartman, S.E.1    Bertone, P.2    Nath, A.K.3    Royce, T.E.4    Gerstein, M.5    Weissman, S.6    Snyder, M.7
  • 16
    • 0345832188 scopus 로고    scopus 로고
    • A chromatin immunoprecipitation screen reveals protein kinase cβ as a direct RUNX1 target gene
    • Hug, B.A., Ahmed, N., Robbins, J.A., and Lazar, M.A. 2004. A chromatin immunoprecipitation screen reveals protein kinase cβ as a direct RUNX1 target gene. J. Biol. Chem. 279: 825-830.
    • (2004) J. Biol. Chem , vol.279 , pp. 825-830
    • Hug, B.A.1    Ahmed, N.2    Robbins, J.A.3    Lazar, M.A.4
  • 18
    • 18744380399 scopus 로고    scopus 로고
    • Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment
    • Kim, J., Bhinge, A.A., Morgan, X.C., and Iyer, V.R. 2005a. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nat. Methods 2: 47-53.
    • (2005) Nat. Methods , vol.2 , pp. 47-53
    • Kim, J.1    Bhinge, A.A.2    Morgan, X.C.3    Iyer, V.R.4
  • 21
    • 0036731485 scopus 로고    scopus 로고
    • Stats: Transcriptional control and biological impact
    • Levy, D.E. and Darnell Jr., J.E. 2002. Stats: Transcriptional control and biological impact. Nat. Rev. Mol. Cell Biol. 3: 651-662.
    • (2002) Nat. Rev. Mol. Cell Biol , vol.3 , pp. 651-662
    • Levy, D.E.1    Darnell Jr., J.E.2
  • 22
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Liu, X., Brutlag, D.L., and Liu, J.S. 2001. BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 127-138.
    • (2001) Pac. Symp. Biocomput , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 23
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
    • Liu, X.S., Brutlag, D.L., and Liu, J.S. 2002. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20: 835-839.
    • (2002) Nat. Biotechnol , vol.20 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 29
    • 0348166011 scopus 로고    scopus 로고
    • Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins
    • Oberley, M.J. and Farnham, P.J. 2003. Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol. 371: 577-596.
    • (2003) Methods Enzymol , vol.371 , pp. 577-596
    • Oberley, M.J.1    Farnham, P.J.2
  • 33
    • 14644406272 scopus 로고    scopus 로고
    • Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping
    • Roh, T.Y., Cuddapah, S., and Zhao, K. 2005. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes & Dev. 19: 542-552.
    • (2005) Genes & Dev , vol.19 , pp. 542-552
    • Roh, T.Y.1    Cuddapah, S.2    Zhao, K.3
  • 34
    • 33645072440 scopus 로고    scopus 로고
    • Service, R.F. 2006. The race for the $1000 genome. Science 311: 1544-1546.
    • Service, R.F. 2006. The race for the $1000 genome. Science 311: 1544-1546.
  • 37
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • Wasserman, W. and Sandelin, A. 2004. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5: 267-287.
    • (2004) Nat. Rev. Genet , vol.5 , pp. 267-287
    • Wasserman, W.1    Sandelin, A.2
  • 39
    • 0034802618 scopus 로고    scopus 로고
    • Use of chromatin immunoprecipitation to clone novel E2F target promoters
    • Weinmann, A.S., Bartley, S.M., Zhang, T., Zhang, M.Q., and Farnham, P.J. 2001. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol. Cell. Biol. 21: 6820-6832.
    • (2001) Mol. Cell. Biol , vol.21 , pp. 6820-6832
    • Weinmann, A.S.1    Bartley, S.M.2    Zhang, T.3    Zhang, M.Q.4    Farnham, P.J.5
  • 40
    • 0037080674 scopus 로고    scopus 로고
    • Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis
    • Weinmann, A.S., Pearlly, S.Y., Oberley, M.J., Huang, T.H.-M., and Farnham, P.J. 2002. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes & Dev. 16: 235-244.
    • (2002) Genes & Dev , vol.16 , pp. 235-244
    • Weinmann, A.S.1    Pearlly, S.Y.2    Oberley, M.J.3    Huang, T.H.-M.4    Farnham, P.J.5
  • 41
    • 33746864004 scopus 로고    scopus 로고
    • ChIP-chip comes of age for genome-wide functional analysis
    • Wu, J., Smith, L.T., Plass, C., and Huang, T.H.-M. 2006. ChIP-chip comes of age for genome-wide functional analysis. Cancer Res. 66: 6899-6902.
    • (2006) Cancer Res , vol.66 , pp. 6899-6902
    • Wu, J.1    Smith, L.T.2    Plass, C.3    Huang, T.H.-M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.