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Volumn 4, Issue 11, 2008, Pages

Analyzing ChIP-chip data using bioconductor

Author keywords

[No Author keywords available]

Indexed keywords

BIOCONDUCTORS; CHIP-CHIP;

EID: 57149119266     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000227     Document Type: Article
Times cited : (16)

References (31)
  • 1
    • 31344436263 scopus 로고    scopus 로고
    • ChIPOTle: A user-friendly tool for the analysis of ChIP-chip data
    • Buck MJ, Nobel AB, Lieb JD (2005) ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biology 6: R97.
    • (2005) Genome Biology , vol.6
    • Buck, M.J.1    Nobel, A.B.2    Lieb, J.D.3
  • 2
    • 24644462724 scopus 로고    scopus 로고
    • TileMap: Create chromosomal map of tiling array hybridizations
    • Ji H, Wong WH (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 21: 3629-3636.
    • (2005) Bioinformatics , vol.21 , pp. 3629-3636
    • Ji, H.1    Wong, W.H.2
  • 4
    • 34247265463 scopus 로고    scopus 로고
    • Mixture modeling for genome-wide localization of transcription factors
    • Keleş S (2007) Mixture modeling for genome-wide localization of transcription factors. Biometrics 63: 10-21.
    • (2007) Biometrics , vol.63 , pp. 10-21
    • Keleş, S.1
  • 11
    • 24044522270 scopus 로고    scopus 로고
    • BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis
    • Durinck S, Moreau Y, Kasprzyk A, Davis S, Moor BD, et al. (2005) BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21: 3439-3440.
    • (2005) Bioinformatics , vol.21 , pp. 3439-3440
    • Durinck, S.1    Moreau, Y.2    Kasprzyk, A.3    Davis, S.4    Moor, B.D.5
  • 12
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
    • Alexa A, Rahnenführer J, Lengauer T (2006) Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607.
    • (2006) Bioinformatics , vol.22 , pp. 1600-1607
    • Alexa, A.1    Rahnenführer, J.2    Lengauer, T.3
  • 14
    • 0004221707 scopus 로고
    • Technical report. StanfordCalifornia: Center for the Study of Language and Information
    • Knuth D (1992) Literate programming. Technical report. StanfordCalifornia: Center for the Study of Language and Information.
    • (1992) Literate programming
    • Knuth, D.1
  • 15
    • 57149085948 scopus 로고    scopus 로고
    • The Microarray and Gene Expression Data (MGED) Society , Available:, Accessed 20 October 2008
    • The Microarray and Gene Expression Data (MGED) Society (2005) MIAME Glossary. Available: http://www.mged.org/Workgroups/MIAME/miame_glossary.html. Accessed 20 October 2008..
    • (2005) MIAME Glossary
  • 17
    • 37349005942 scopus 로고    scopus 로고
    • Combinatorial effects of four histone modifications in transcription and differentiation
    • Fischer JJ, Toedling J, Krueger T, Schueler M, Huber W, et al. (2008) Combinatorial effects of four histone modifications in transcription and differentiation. Genomics 91: 41-51.
    • (2008) Genomics , vol.91 , pp. 41-51
    • Fischer, J.J.1    Toedling, J.2    Krueger, T.3    Schueler, M.4    Huber, W.5
  • 18
    • 38049054726 scopus 로고    scopus 로고
    • Genomewide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
    • Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, et al. (2008) Genomewide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res 18: 46-59.
    • (2008) Genome Res , vol.18 , pp. 46-59
    • Barrera, L.O.1    Li, Z.2    Smith, A.D.3    Arden, K.C.4    Cavenee, W.K.5
  • 19
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 20
    • 33644872577 scopus 로고    scopus 로고
    • eds () Bioinformatics and Computational Biology Solutions Using R and BioconductorSpringer. pp
    • Smyth GK (2005) Limma: linear models for microarray data. In: Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S, eds (2005) Bioinformatics and Computational Biology Solutions Using R and BioconductorSpringer. pp 397-420.
    • (2005) Limma: Linear models for microarray data , pp. 397-420
    • Smyth, G.K.1
  • 21
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater GSC, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.C.1    Birney, E.2
  • 23
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
    • (2000) Nat Genet , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4    Butler, H.5
  • 24
    • 33747856481 scopus 로고    scopus 로고
    • Transcript mapping with high-density oligonucleotide tiling arrays
    • Huber W, Toedling J, Steinmetz LM (2006) Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 22: 1963-1970.
    • (2006) Bioinformatics , vol.22 , pp. 1963-1970
    • Huber, W.1    Toedling, J.2    Steinmetz, L.M.3
  • 25
    • 0030597343 scopus 로고    scopus 로고
    • A novel gene family defined by human dihydropyrimidinase and three related proteins with differential tissue distribution
    • Hamajima N, Matsuda K, Sakata S, Tamaki N, Sasaki M, et al. (1996) A novel gene family defined by human dihydropyrimidinase and three related proteins with differential tissue distribution. Gene 180: 157-163.
    • (1996) Gene , vol.180 , pp. 157-163
    • Hamajima, N.1    Matsuda, K.2    Sakata, S.3    Tamaki, N.4    Sasaki, M.5
  • 26
    • 34249730556 scopus 로고    scopus 로고
    • Assessing the need for sequence-based normalization in tiling microarray experiments
    • Royce TE, Rozowsky JS, Gerstein MB (2007) Assessing the need for sequence-based normalization in tiling microarray experiments. Bioinformatics 23: 988-997.
    • (2007) Bioinformatics , vol.23 , pp. 988-997
    • Royce, T.E.1    Rozowsky, J.S.2    Gerstein, M.B.3
  • 27
    • 33745225872 scopus 로고    scopus 로고
    • Genomewide analysis of Polycomb targets in Drosophila melanogaster
    • Schwartz YB, Kahn TG, Nix DA, Li XY, Bourgon R, et al. (2006) Genomewide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 38: 700-705.
    • (2006) Nat Genet , vol.38 , pp. 700-705
    • Schwartz, Y.B.1    Kahn, T.G.2    Nix, D.A.3    Li, X.Y.4    Bourgon, R.5
  • 28
    • 57149083750 scopus 로고    scopus 로고
    • Bourgon RW (2006) Chromatin-immunoprecipitation and high-density tiling microarrays: a generative model, methods for analysis, and methodology assessment in the absence of a gold standard. Ph.D. thesis, University of California Berkeley, Berkeley, California, United States of America. Available: http://www.ebi.ac.uk/~bourgon/papers/ bourgon_dissertation_public.pdf. Accessed 20 October 2008..
    • Bourgon RW (2006) Chromatin-immunoprecipitation and high-density tiling microarrays: a generative model, methods for analysis, and methodology assessment in the absence of a "gold standard". Ph.D. thesis, University of California Berkeley, Berkeley, California, United States of America. Available: http://www.ebi.ac.uk/~bourgon/papers/ bourgon_dissertation_public.pdf. Accessed 20 October 2008..
  • 29
    • 40549114662 scopus 로고    scopus 로고
    • CMARRT: A tool for the analysis of ChIPchip data from tiling arrays by incorporating the correlation structure
    • Kuan PF, Chun H, Keleş S (2008) CMARRT: a tool for the analysis of ChIPchip data from tiling arrays by incorporating the correlation structure. Pac Symp Biocomput 2008: 515-526.
    • (2008) Pac Symp Biocomput 2008 , pp. 515-526
    • Kuan, P.F.1    Chun, H.2    Keleş, S.3
  • 30
    • 0030921594 scopus 로고    scopus 로고
    • A database for post-genome analysis
    • Kanehisa M (1997) A database for post-genome analysis. Trends Genet 13: 375-376.
    • (1997) Trends Genet , vol.13 , pp. 375-376
    • Kanehisa, M.1
  • 31
    • 33747874899 scopus 로고    scopus 로고
    • Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays
    • Scacheri PC, Crawford GE, Davis S (2006) Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol 411: 270-282.
    • (2006) Methods Enzymol , vol.411 , pp. 270-282
    • Scacheri, P.C.1    Crawford, G.E.2    Davis, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.