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Volumn 5, Issue , 2015, Pages

Sandcastle: Software for revealing latent information in multiple experimental ChIP-chip datasets via a novel normalisation procedure

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AUTOMATED PATTERN RECOGNITION; CHROMATIN IMMUNOPRECIPITATION; COMPUTER LANGUAGE; COMPUTER SIMULATION; DATA MINING; EVALUATION STUDY; GENETIC DATABASE; HIGH THROUGHPUT SEQUENCING; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SOFTWARE; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 84940069144     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep13395     Document Type: Article
Times cited : (4)

References (25)
  • 1
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of DNA binding proteins
    • Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306 (2000).
    • (2000) Science , vol.290 , pp. 2306
    • Ren, B.1
  • 2
    • 0037172993 scopus 로고    scopus 로고
    • Methylation of histone H3 Lys 4 in coding regions of active genes
    • Bernstein, B. et al. Methylation of histone H3 Lys 4 in coding regions of active genes. P Natl Acad Sci USA 99, 8695 (2002).
    • (2002) P Natl Acad Sci USA , vol.99 , pp. 8695
    • Bernstein, B.1
  • 3
    • 23944462969 scopus 로고    scopus 로고
    • Genome-wide map of nucleosome acetylation and methylation in yeast
    • Pokholok, D. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517-527 (2005).
    • (2005) Cell , vol.122 , pp. 517-527
    • Pokholok, D.1
  • 4
    • 34748826166 scopus 로고    scopus 로고
    • A high-resolution atlas of nucleosome occupancy in yeast
    • Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39, 1235-1244 (2007).
    • (2007) Nat Genet , vol.39 , pp. 1235-1244
    • Lee, W.1
  • 5
    • 79551497695 scopus 로고    scopus 로고
    • A novel method for the genome-wide high resolution analysis of DNA damage
    • Teng, Y. et al. A novel method for the genome-wide high resolution analysis of DNA damage. Nucleic Acids Res 39, e10 (2011).
    • (2011) Nucleic Acids Res , vol.39 , pp. e10
    • Teng, Y.1
  • 6
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • Buck, M., Lieb, J. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83, 349-360 (2004).
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.1    Lieb, J.2
  • 7
    • 40449126726 scopus 로고    scopus 로고
    • Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
    • Johnson, D. et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res 18, 393 (2008).
    • (2008) Genome Res , vol.18 , pp. 393
    • Johnson, D.1
  • 8
    • 48249151081 scopus 로고    scopus 로고
    • Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast
    • Schlecht, U. et al. Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. Mol Biol Cell 19, 2193-2207 (2008).
    • (2008) Mol Biol Cell , vol.19 , pp. 2193-2207
    • Schlecht, U.1
  • 9
    • 57349109349 scopus 로고    scopus 로고
    • CARPET: A web-based package for the analysis of ChIP-chip and expression tiling data
    • Cesaroni, M., Cittaro, D., Brozzi, A., Pelicci, P., Luzi, L. CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data. Bioinformatics 24, 2918 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 2918
    • Cesaroni, M.1    Cittaro, D.2    Brozzi, A.3    Pelicci, P.4    Luzi, L.5
  • 10
    • 77951962216 scopus 로고    scopus 로고
    • Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
    • Johannes, F. et al. Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq. Bioinformatics 26, 1000 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 1000
    • Johannes, F.1
  • 11
    • 77955016494 scopus 로고    scopus 로고
    • JAMIE: Joint analysis of multiple ChIP-chip experiments
    • Wu, H., Ji, H. JAMIE: joint analysis of multiple ChIP-chip experiments. Bioinformatics 26, 1864 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 1864
    • Wu, H.1    Ji, H.2
  • 12
    • 34249853277 scopus 로고    scopus 로고
    • DNA demethylation in the Arabidopsis genome
    • Penterman, J. et al. DNA demethylation in the Arabidopsis genome. Proc Natl Acad Sci USA 104, 6752 (2007).
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 6752
    • Penterman, J.1
  • 13
    • 45349086923 scopus 로고    scopus 로고
    • Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes
    • Farthing, C. et al. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet 4, e1000116 (2008).
    • (2008) PLoS Genet , vol.4 , pp. e1000116
    • Farthing, C.1
  • 14
    • 77951962649 scopus 로고    scopus 로고
    • ChIPMonk: Software for viewing and analysing ChIP-on-chip data
    • Andrews, S. ChIPMonk: software for viewing and analysing ChIP-on-chip data. BMC Syst Biol 1, P80 (2007).
    • (2007) BMC Syst Biol , vol.1 , pp. P80
    • Andrews, S.1
  • 15
    • 34447277157 scopus 로고    scopus 로고
    • Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts
    • Toedling, J., Sklyar, O., Huber, W. Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics. 8, 221 (2007).
    • (2007) BMC Bioinformatics , vol.8 , pp. 221
    • Toedling, J.1    Sklyar, O.2    Huber, W.3
  • 16
    • 34548300744 scopus 로고    scopus 로고
    • Tilescope: Online analysis pipeline for high-density tiling microarray data
    • Zhang, Z. et al. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol 8, R81 (2007).
    • (2007) Genome Biol , vol.8 , pp. R81
    • Zhang, Z.1
  • 17
    • 0036898577 scopus 로고    scopus 로고
    • Microarray data normalization and transformation
    • Quackenbush, J. Microarray data normalization and transformation. Nature Genet. 32, 496-501 (2002).
    • (2002) Nature Genet , vol.32 , pp. 496-501
    • Quackenbush, J.1
  • 18
    • 57149089456 scopus 로고    scopus 로고
    • Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies
    • Ponzielli, R. et al. Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res. 36, e144 (2008).
    • (2008) Nucleic Acids Res , vol.36 , pp. e144
    • Ponzielli, R.1
  • 20
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad, B., Irizarry, R., Åstrand, M., Speed, T. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 19, 185 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 185
    • Bolstad, B.1    Irizarry, R.2    Åstrand, M.3    Speed, T.4
  • 21
    • 31344436263 scopus 로고    scopus 로고
    • ChIPOTle: A user-friendly tool for the analysis of ChIP-chip data
    • Buck, M., Nobel, A., Lieb, J. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 6, R97 (2005).
    • (2005) Genome Biol , vol.6 , pp. R97
    • Buck, M.1    Nobel, A.2    Lieb, J.3
  • 22
    • 71849096141 scopus 로고    scopus 로고
    • How does multiple testing correction work
    • Noble, W. S. How does multiple testing correction work? Nat Biotechnol. 27, 1135-1137 (2009).
    • (2009) Nat Biotechnol , vol.27 , pp. 1135-1137
    • Noble, W.S.1
  • 23
    • 24044522270 scopus 로고    scopus 로고
    • BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis
    • Durinck, S. et al. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics. 21, 3439-3440 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 3439-3440
    • Durinck, S.1
  • 24
    • 37849051645 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae Rad16 mediates ultraviolet-dependent histone H3 acetylation required for efficient global genome nucleotide-excision repair
    • Teng, Y. et al. Saccharomyces cerevisiae Rad16 mediates ultraviolet-dependent histone H3 acetylation required for efficient global genome nucleotide-excision repair. EMBO Rep. 9, 97-102 (2007).
    • (2007) EMBO Rep , vol.9 , pp. 97-102
    • Teng, Y.1
  • 25
    • 79959843190 scopus 로고    scopus 로고
    • How chromatin is remodelled during DNA repair of UV-induced DNA damage in Saccharomyces cerevisiae
    • Yu, S., Teng, Y., Waters, R., Reed, H. How chromatin is remodelled during DNA repair of UV-induced DNA damage in Saccharomyces cerevisiae. PLoS Genet. 7, doi: 10.1371/journal.pgen.1002124 (2011).
    • (2011) PLoS Genet , vol.7
    • Yu, S.1    Teng, Y.2    Waters, R.3    Reed, H.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.