메뉴 건너뛰기




Volumn 29, Issue 15, 2013, Pages 1851-1857

Gene-set analysis is severely biased when applied to genome-wide methylation data

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; GENE; GENETICS; GENOMICS; HUMAN; LUNG TUMOR; METHODOLOGY; ULCERATIVE COLITIS; PROCEDURES;

EID: 84880544162     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt311     Document Type: Article
Times cited : (105)

References (36)
  • 2
    • 18744389489 scopus 로고    scopus 로고
    • Significance analysis of functional categories in gene expression studies: A structured permutation approach
    • DOI 10.1093/bioinformatics/bti260
    • Barry, W. et al. (2005) Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics, 21, 1943-1949. (Pubitemid 40668030)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1943-1949
    • Barry, W.T.1    Nobel, A.B.2    Wright, F.A.3
  • 3
    • 79960688508 scopus 로고    scopus 로고
    • DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
    • Bell, J. et al. (2011) DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol., 12, R10.
    • (2011) Genome Biol. , vol.12
    • Bell, J.1
  • 4
    • 84861221693 scopus 로고    scopus 로고
    • Quantitative sequencing of 5-methylcytosine and 5-hydro-xymethylcytosine at single-base resolution
    • Booth, M.J. et al. (2012) Quantitative sequencing of 5-methylcytosine and 5-hydro-xymethylcytosine at single-base resolution. Science, 336, 934-937.
    • (2012) Science , vol.336 , pp. 934-937
    • Booth, M.J.1
  • 5
    • 84864071185 scopus 로고    scopus 로고
    • Quantitative DNA methylation analysis identifies a single CpG dinucleotide important for ZAP-70 expression and predictive of prognosis in chronic lymphocytic leukemia
    • Claus, R. et al. (2012) Quantitative DNA methylation analysis identifies a single CpG dinucleotide important for ZAP-70 expression and predictive of prognosis in chronic lymphocytic leukemia. J. Clin. Oncol., 30, 2483-2491.
    • (2012) J. Clin. Oncol. , vol.30 , pp. 2483-2491
    • Claus, R.1
  • 6
    • 0033135049 scopus 로고    scopus 로고
    • Methylation of CpG in a small region of the hMLH1 promoter invariably correlates with the absence of gene expression
    • Deng, G. et al. (1999) Methylation of CpG in a small region of the hMLH1 promoter invariably correlates with the absence of gene expression. Cancer Res., 59, 2029-2033. (Pubitemid 29217657)
    • (1999) Cancer Research , vol.59 , Issue.9 , pp. 2029-2033
    • Deng, G.1    Chen, A.2    Hong, J.3    Chae, H.S.4    Kim, Y.S.5
  • 7
    • 64349106730 scopus 로고    scopus 로고
    • Targeted bisulfite sequencing reveals changes in DNA methy-lation associated with nuclear reprogramming
    • Deng, J. et al. (2009) Targeted bisulfite sequencing reveals changes in DNA methy-lation associated with nuclear reprogramming. Nat. Biotechnol., 27, 353-360.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 353-360
    • Deng, J.1
  • 8
    • 70649095120 scopus 로고    scopus 로고
    • Differential methylation of tissue- and cancer-specific CpG Island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
    • Doi, A. et al. (2009) Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet., 41, 1350-1353.
    • (2009) Nat. Genet. , vol.41 , pp. 1350-1353
    • Doi, A.1
  • 9
    • 77950416884 scopus 로고    scopus 로고
    • A genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers
    • Dunwell, T. et al. (2010) A genome-wide screen identifies frequently methylated genes in haematological and epithelial cancers. Mol. Cancer, 9, 44.
    • (2010) Mol. Cancer , vol.9 , pp. 44
    • Dunwell, T.1
  • 10
    • 0035080617 scopus 로고    scopus 로고
    • The risk of colorectal cancer in ulcerative colitis: A meta-analysis
    • DOI 10.1136/gut.48.4.526
    • Eaden, J. et al. (2001) The risk of colorectal cancer in ulcerative colitis: a meta-analysis. Gut, 48, 526-535. (Pubitemid 32234798)
    • (2001) Gut , vol.48 , Issue.4 , pp. 526-535
    • Eaden, J.A.1    Abrams, K.R.2    Mayberry, J.F.3
  • 11
    • 35348890683 scopus 로고    scopus 로고
    • On testing the significance of sets of genes
    • Efron, B. and Tibshirani, R. (2007) On testing the significance of sets of genes. Ann. Appl. Stat., 1, 107-129.
    • (2007) Ann. Appl. Stat. , vol.1 , pp. 107-129
    • Efron, B.1    Tibshirani, R.2
  • 12
    • 67650488920 scopus 로고    scopus 로고
    • DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, apis mellifera
    • Elango, N. et al. (2009) DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera. Proc. Natl Acad. Sci. USA, 106, 11206-11211.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 11206-11211
    • Elango, N.1
  • 13
    • 33846689706 scopus 로고    scopus 로고
    • Using GOstats to test gene lists for GO term association
    • DOI 10.1093/bioinformatics/btl567
    • Falcon, S. and Gentleman, R. (2007) Using gostats to test gene lists for go term association. Bioinformatics, 23, 257-258. (Pubitemid 46189622)
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 257-258
    • Falcon, S.1    Gentleman, R.2
  • 14
    • 84857785696 scopus 로고    scopus 로고
    • DNA hypermethylation in lung cancer is targeted at differentiation- associated genes
    • Helman, E. et al. (2012) DNA hypermethylation in lung cancer is targeted at differentiation-associated genes. Oncogene, 31, 1181-1188.
    • (2012) Oncogene , vol.31 , pp. 1181-1188
    • Helman, E.1
  • 15
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang, D.W. et al. (2009a) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1
  • 16
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using david bioinformatics resources
    • Huang, D.W. et al. (2009b) Systematic and integrative analysis of large gene lists using david bioinformatics resources. Nat. Protoc., 4, 44-57.
    • (2009) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1
  • 17
    • 59149084538 scopus 로고    scopus 로고
    • The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG Island shores
    • Irizarry, R.A. et al. (2009) The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.
    • (2009) Nat. Genet. , vol.41 , pp. 178-186
    • Irizarry, R.A.1
  • 18
    • 84880921962 scopus 로고    scopus 로고
    • The DNA methylation landscape of small cell lung cancer suggests a differentiation defect of neuroendocrine cells
    • [Epub ahead of print, doi: 10.1038/onc.2012.362, August 20, 2012]
    • Kalari, S. et al. (2012) The DNA methylation landscape of small cell lung cancer suggests a differentiation defect of neuroendocrine cells. Oncogene [Epub ahead of print, doi: 10.1038/onc.2012.362, August 20, 2012].
    • (2012) Oncogene
    • Kalari, S.1
  • 19
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30. (Pubitemid 30047706)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 20
    • 77956311283 scopus 로고    scopus 로고
    • A study of the influence of sex on genome wide methylation
    • Liu, J. et al. (2010) A study of the influence of sex on genome wide methylation. PLoS One, 5, e10028.
    • (2010) PLoS One , vol.5
    • Liu, J.1
  • 21
    • 77952214662 scopus 로고    scopus 로고
    • Great improves functional interpretation of cis-regulatory regions
    • McLean, C.Y. et al. (2010) Great improves functional interpretation of cis-regulatory regions. Nat. Biotechnol., 28, 495-501.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 495-501
    • McLean, C.Y.1
  • 22
    • 61449426211 scopus 로고    scopus 로고
    • Methylated DNA immunoprecipitation (medip)
    • Mohn, F. et al. (2009) Methylated DNA immunoprecipitation (medip). Methods Mol. Biol., 507, 55-64.
    • (2009) Methods Mol. Biol. , vol.507 , pp. 55-64
    • Mohn, F.1
  • 23
    • 67651149735 scopus 로고    scopus 로고
    • High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
    • Oda, M. et al. (2009) High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res., 37, 3829-3839.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3829-3839
    • Oda, M.1
  • 24
    • 65649126066 scopus 로고    scopus 로고
    • Transcript length bias in RNA-seq data confounds systems biology
    • Oshlack, A. and Wakefield, M.J. (2009) Transcript length bias in RNA-seq data confounds systems biology. Biol. Direct, 4, 14.
    • (2009) Biol. Direct , vol.4 , pp. 14
    • Oshlack, A.1    Wakefield, M.J.2
  • 25
    • 38349135680 scopus 로고    scopus 로고
    • High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer
    • Rauch, T.A. et al. (2008) High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc. Natl Acad. Sci. USA, 105, 252-257.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 252-257
    • Rauch, T.A.1
  • 26
    • 80053493397 scopus 로고    scopus 로고
    • Large-scale methylation domains mark a functional subset of neuronally expressed genes
    • Schroeder, D.I. et al. (2011) Large-scale methylation domains mark a functional subset of neuronally expressed genes. Genome Res., 21, 1583-1591.
    • (2011) Genome Res. , vol.21 , pp. 1583-1591
    • Schroeder, D.I.1
  • 27
    • 75749104729 scopus 로고    scopus 로고
    • DNMT1 maintains progenitor function in self-renewing somatic tissue
    • Sen, G.L. et al. (2010) DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature, 463, 563-567.
    • (2010) Nature , vol.463 , pp. 563-567
    • Sen, G.L.1
  • 29
    • 77951667118 scopus 로고    scopus 로고
    • Functional switching of TGF-beta1 signaling in liver cancer via epigenetic modulation of a single CpG site in TTP promoter
    • Sohn, B.H. et al. (2010) Functional switching of TGF-beta1 signaling in liver cancer via epigenetic modulation of a single CpG site in TTP promoter. Gastroenterology, 138, 1898-1908.
    • (2010) Gastroenterology , vol.138 , pp. 1898-1908
    • Sohn, B.H.1
  • 30
    • 84866844032 scopus 로고    scopus 로고
    • Tissue of origin determines cancer-associated CpG Island promoter hypermethylation patterns
    • Sproul, D. et al. (2012) Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns. Genome Biol., 13, R84.
    • (2012) Genome Biol. , vol.13
    • Sproul, D.1
  • 32
    • 70350069495 scopus 로고    scopus 로고
    • The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG Islands
    • Takeshima, H. et al. (2009) The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands. Genome Res., 19, 1974-1982.
    • (2009) Genome Res. , vol.19 , pp. 1974-1982
    • Takeshima, H.1
  • 33
    • 23044514626 scopus 로고    scopus 로고
    • Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
    • DOI 10.1038/ng1598
    • Weber, M. et al. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet., 37, 853-862. (Pubitemid 41077111)
    • (2005) Nature Genetics , vol.37 , Issue.8 , pp. 853-862
    • Weber, M.1    Davies, J.J.2    Wittig, D.3    Oakeley, E.J.4    Haase, M.5    Lam, W.L.6    Schubeler, D.7
  • 34
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-seq: Accounting for selection bias
    • Young, M.D. et al. (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol., 11, R14.
    • (2010) Genome Biol. , vol.11
    • Young, M.D.1
  • 35
    • 84859853844 scopus 로고    scopus 로고
    • Differential DNA methylation status between human prea-dipocytes and mature adipocytes
    • Zhu, J.G. et al. (2012) Differential DNA methylation status between human prea-dipocytes and mature adipocytes. Cell Biochem. Biophys., 63, 1-15.
    • (2012) Cell Biochem. Biophys. , vol.63 , pp. 1-15
    • Zhu, J.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.