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Volumn 16, Issue 5, 2015, Pages

Using epigenomics data to predict gene expression in lung cancer

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; ARTIFICIAL INTELLIGENCE; BIOLOGICAL ORGANS; DECISION TREES; DISEASES; FEATURE EXTRACTION; FORECASTING; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENES; LEARNING SYSTEMS; METHYLATION;

EID: 84961509372     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-16-S5-S10     Document Type: Article
Times cited : (49)

References (33)
  • 1
    • 77957970301 scopus 로고    scopus 로고
    • Epigenetic modifications and human disease
    • Portela A, Esteller M: Epigenetic modifications and human disease. Nature biotechnology. 2010, 28 (10): 1057-1068. 10.1038/nbt.1685.
    • (2010) Nature biotechnology , vol.28 , Issue.10 , pp. 1057-1068
    • Portela, A.1    Esteller, M.2
  • 2
    • 37548999369 scopus 로고    scopus 로고
    • Computational epigenetics
    • Bock C, Lengauer T: Computational epigenetics. Bioinformatics. 2008, 24 (1): 1-10. 10.1093/bioinformatics/btm546.
    • (2008) Bioinformatics , vol.24 , Issue.1 , pp. 1-10
    • Bock, C.1    Lengauer, T.2
  • 3
    • 77249137168 scopus 로고    scopus 로고
    • Principles and challenges of genomewide DNA methylation analysis
    • Laird PW: Principles and challenges of genomewide DNA methylation analysis. Nature reviews Genetics. 2010, 11 (3): 191-203. 10.1038/nrg2732.
    • (2010) Nature reviews Genetics , vol.11 , Issue.3 , pp. 191-203
    • Laird, P.W.1
  • 4
    • 79956335673 scopus 로고    scopus 로고
    • Computational Epigenetics: the new scientific paradigm
    • Lim SJ, Tan TW, Tong JC: Computational Epigenetics: the new scientific paradigm. Bioinformation. 2010, 4 (7): 331-337. 10.6026/97320630004331.
    • (2010) Bioinformation , vol.4 , Issue.7 , pp. 331-337
    • Lim, S.J.1    Tan, T.W.2    Tong, J.C.3
  • 5
  • 6
    • 78650580072 scopus 로고    scopus 로고
    • Specific gene hypomethylation and cancer: New insights into coding region feature trends
    • Daura-Oller E, Cabre M, Montero MA, Paternain JL, Romeu A: Specific gene hypomethylation and cancer: New insights into coding region feature trends. Bioinformation. 2009, 3 (8): 340-10.6026/97320630003340.
    • (2009) Bioinformation , vol.3 , Issue.8 , pp. 340
    • Daura-Oller, E.1    Cabre, M.2    Montero, M.A.3    Paternain, J.L.4    Romeu, A.5
  • 7
    • 77955700020 scopus 로고    scopus 로고
    • Genome-wide hypomethylation in cancer may be a passive consequence of transformation
    • Wild L, Flanagan JM: Genome-wide hypomethylation in cancer may be a passive consequence of transformation. Biochimica et biophysica acta. 2010, 1806 (1): 50-57.
    • (2010) Biochimica et biophysica acta , vol.1806 , Issue.1 , pp. 50-57
    • Wild, L.1    Flanagan, J.M.2
  • 9
    • 84885905391 scopus 로고    scopus 로고
    • Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer
    • Rhee JK, Kim K, Chae H, Evans J, Yan P, Zhang BT, Gray J, Spellman P, Huang TH, Nephew KP, et al: Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer. Nucleic acids research. 2013, 41 (18): 8464-8474. 10.1093/nar/gkt643.
    • (2013) Nucleic acids research , vol.41 , Issue.18 , pp. 8464-8474
    • Rhee, J.K.1    Kim, K.2    Chae, H.3    Evans, J.4    Yan, P.5    Zhang, B.T.6    Gray, J.7    Spellman, P.8    Huang, T.H.9    Nephew, K.P.10
  • 10
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • An integrated encyclopedia of DNA elements in the human genome. Nature. 2012, 489 (7414): 57-74. 10.1038/nature11247.
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 12
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nature methods. 2012, 9 (4): 357-359. 10.1038/nmeth.1923.
    • (2012) Nature methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 14
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26 (6): 841-842. 10.1093/bioinformatics/btq033.
    • (2010) Bioinformatics , vol.26 , Issue.6 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 16
    • 84908535418 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
    • bioRxiv
    • Love MI, Huber W, Anders S: Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. bioRxiv. 2014
    • (2014)
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 17
    • 0002294347 scopus 로고
    • A simple sequentially rejective multiple test procedure
    • Holm S: A simple sequentially rejective multiple test procedure. Scandinavian journal of statistics. 1979, 65-70.
    • (1979) Scandinavian journal of statistics , pp. 65-70
    • Holm, S.1
  • 19
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26 (6): 841-842. 10.1093/bioinformatics/btq033.
    • (2010) Bioinformatics , vol.26 , Issue.6 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 20
    • 84977650745 scopus 로고    scopus 로고
    • String objects representing biological sequences, and matching algorithms
    • R package version
    • Pages H, Aboyoun P, Gentleman R, DebRoy S: String objects representing biological sequences, and matching algorithms. R package version. 2009, 2 (2):
    • (2009) , vol.2 , Issue.2
    • Pages, H.1    Aboyoun, P.2    Gentleman, R.3    DebRoy, S.4
  • 21
    • 4043059226 scopus 로고    scopus 로고
    • Feature Selection for Machine Learning: Comparing a Correlation-Based Filter Approach to the Wrapper
    • Hall MA, Smith LA: Feature Selection for Machine Learning: Comparing a Correlation-Based Filter Approach to the Wrapper. FLAIRS Conference: 1999. 1999, 235-239.
    • (1999) FLAIRS Conference , vol.1999 , pp. 235-239
    • Hall, M.A.1    Smith, L.A.2
  • 22
    • 33744584654 scopus 로고
    • Induction of decision trees
    • Quinlan JR: Induction of decision trees. Machine learning. 1986, 1 (1): 81-106.
    • (1986) Machine learning , vol.1 , Issue.1 , pp. 81-106
    • Quinlan, J.R.1
  • 23
    • 0030735972 scopus 로고    scopus 로고
    • Overcoming the Myopia of Inductive Learning Algorithms with RELIEFF
    • Kononenko I, Šimec E, Robnik-Šikonja M: Overcoming the Myopia of Inductive Learning Algorithms with RELIEFF. Applied Intelligence. 1997, 7 (1): 39-55. 10.1023/A:1008280620621.
    • (1997) Applied Intelligence , vol.7 , Issue.1 , pp. 39-55
    • Kononenko, I.1    Šimec, E.2    Robnik-Šikonja, M.3
  • 24
    • 0027002164 scopus 로고
    • The feature selection problem: Traditional methods and a new algorithm
    • Kira K, Rendell LA: The feature selection problem: Traditional methods and a new algorithm. AAAI: 1992. 1992, 129-134.
    • (1992) AAAI 1992 , pp. 129-134
    • Kira, K.1    Rendell, L.A.2
  • 26
    • 84886047856 scopus 로고    scopus 로고
    • Corrplot: visualization of a correlation matrix
    • R package version 02-0 Available on Comprehensive R Archive Network website. , (accessed 2010)
    • Wei T: Corrplot: visualization of a correlation matrix. R package version 02-0 Available on Comprehensive R Archive Network website. 2010, (accessed 2010), [ http://CRANR-project.org/package=corrplot ]
    • (2010)
    • Wei, T.1
  • 27
    • 27544491192 scopus 로고    scopus 로고
    • ROCR: visualizing classifier performance in R
    • Sing T, Sander O, Beerenwinkel N, Lengauer T: ROCR: visualizing classifier performance in R. Bioinformatics. 2005, 21 (20): 3940-3941. 10.1093/bioinformatics/bti623.
    • (2005) Bioinformatics , vol.21 , Issue.20 , pp. 3940-3941
    • Sing, T.1    Sander, O.2    Beerenwinkel, N.3    Lengauer, T.4
  • 28
    • 0037423186 scopus 로고    scopus 로고
    • The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation
    • Fuks F, Hurd PJ, Wolf D, Nan X, Bird AP, Kouzarides T: The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. Journal of Biological Chemistry. 2003, 278 (6): 4035-4040. 10.1074/jbc.M210256200.
    • (2003) Journal of Biological Chemistry , vol.278 , Issue.6 , pp. 4035-4040
    • Fuks, F.1    Hurd, P.J.2    Wolf, D.3    Nan, X.4    Bird, A.P.5    Kouzarides, T.6
  • 29
    • 67349190247 scopus 로고    scopus 로고
    • Linking DNA methylation and histone modification: patterns and paradigms
    • Cedar H, Bergman Y: Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009, 10 (5): 295-304. 10.1038/nrg2540.
    • (2009) Nat Rev Genet , vol.10 , Issue.5 , pp. 295-304
    • Cedar, H.1    Bergman, Y.2
  • 30
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: islands, start sites, gene bodies and beyond
    • Jones PA: Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012, 13 (7): 484-492. 10.1038/nrg3230.
    • (2012) Nat Rev Genet , vol.13 , Issue.7 , pp. 484-492
    • Jones, P.A.1
  • 32
    • 4644328089 scopus 로고    scopus 로고
    • Chromosomal regulation by MeCP2: structural and enzymatic considerations
    • Bowen NJ, Palmer MB, Wade PA: Chromosomal regulation by MeCP2: structural and enzymatic considerations. Cellular and molecular life sciences: CMLS. 2004, 61 (17): 2163-2167.
    • (2004) Cellular and molecular life sciences: CMLS , vol.61 , Issue.17 , pp. 2163-2167
    • Bowen, N.J.1    Palmer, M.B.2    Wade, P.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.