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Volumn 104, Issue 4, 2014, Pages 229-233

Prediction of CpG island methylation status by integrating DNA physicochemical properties

Author keywords

CpG island; DNA methylation; DNA physicochemical property; Na ve Bayes; Pseudo trinucleotide composition

Indexed keywords

ARTICLE; BAYESIAN LEARNING; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CPG ISLAND; DNA BASE COMPOSITION; DNA METHYLATION; DNA PHYSICOCHEMICAL PROPERTY; DNA SEQUENCE; HEART MUSCLE; JACKKNIFE TEST; PHYSICAL CHEMISTRY; PREDICTION; PSEUDO TRINUCLEOTIDE COMPOSITION; BAYES THEOREM; CHEMISTRY; GENETIC EPIGENESIS; HUMAN; HUMAN GENOME; PROCEDURES;

EID: 84908214945     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2014.08.011     Document Type: Article
Times cited : (36)

References (37)
  • 1
    • 0022540321 scopus 로고
    • CpG-rich islands and the function of DNA methylation
    • Bird A.P. CpG-rich islands and the function of DNA methylation. Nature 1986, 321:209-213.
    • (1986) Nature , vol.321 , pp. 209-213
    • Bird, A.P.1
  • 2
    • 0037372003 scopus 로고    scopus 로고
    • Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals
    • (Suppl.)
    • Jaenisch R., Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 2003, 33:245-254. (Suppl.).
    • (2003) Nat. Genet. , vol.33 , pp. 245-254
    • Jaenisch, R.1    Bird, A.2
  • 6
    • 16544395591 scopus 로고    scopus 로고
    • DNA methylation and cancer
    • Das P.M., Singal R. DNA methylation and cancer. J. Clin. Oncol. 2004, 22:4632-4642.
    • (2004) J. Clin. Oncol. , vol.22 , pp. 4632-4642
    • Das, P.M.1    Singal, R.2
  • 7
    • 80054994283 scopus 로고    scopus 로고
    • Identification of genetic elements that autonomously determine DNA methylation states
    • Lienert F., Wirbelauer C., Som I., Dean A., Mohn F., Schubeler D. Identification of genetic elements that autonomously determine DNA methylation states. Nat. Genet. 2011, 43:1091-1097.
    • (2011) Nat. Genet. , vol.43 , pp. 1091-1097
    • Lienert, F.1    Wirbelauer, C.2    Som, I.3    Dean, A.4    Mohn, F.5    Schubeler, D.6
  • 8
    • 0032890965 scopus 로고    scopus 로고
    • The DNA methylation paradox
    • Jones P.A. The DNA methylation paradox. Trends Genet. 1999, 15:34-37.
    • (1999) Trends Genet. , vol.15 , pp. 34-37
    • Jones, P.A.1
  • 9
    • 84863986133 scopus 로고    scopus 로고
    • Functions of DNA methylation: islands, start sites, gene bodies and beyond
    • Jones P.A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 2012, 13:484-492.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 13
    • 23044514626 scopus 로고    scopus 로고
    • Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells
    • Weber M., Davies J.J., Wittig D., Oakeley E.J., Haase M., Lam W.L., Schubeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 2005, 37:853-862.
    • (2005) Nat. Genet. , vol.37 , 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
  • 14
    • 23644439586 scopus 로고    scopus 로고
    • Prediction of methylated CpGs in DNA sequences using a support vector machine
    • Bhasin M., Zhang H., Reinherz E.L., Reche P.A. Prediction of methylated CpGs in DNA sequences using a support vector machine. FEBS Lett. 2005, 579:4302-4308.
    • (2005) FEBS Lett. , vol.579 , pp. 4302-4308
    • Bhasin, M.1    Zhang, H.2    Reinherz, E.L.3    Reche, P.A.4
  • 16
    • 84872923864 scopus 로고    scopus 로고
    • CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome
    • Zheng H., Wu H., Li J., Jiang S.W. CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome. BMC Med. Genomics 2013, 6(Suppl. 1):S13.
    • (2013) BMC Med. Genomics , vol.6 , pp. S13
    • Zheng, H.1    Wu, H.2    Li, J.3    Jiang, S.W.4
  • 18
  • 19
    • 79951518208 scopus 로고    scopus 로고
    • Some remarks on protein attribute prediction and pseudo amino acid composition
    • Chou K.C. Some remarks on protein attribute prediction and pseudo amino acid composition. J. Theor. Biol. 2011, 273:236-247.
    • (2011) J. Theor. Biol. , vol.273 , pp. 236-247
    • Chou, K.C.1
  • 20
    • 33747197197 scopus 로고    scopus 로고
    • Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers
    • Chou K.C., Shen H.B. Predicting eukaryotic protein subcellular location by fusing optimized evidence-theoretic K-Nearest Neighbor classifiers. J. Proteome Res. 2006, 5:1888-1897.
    • (2006) J. Proteome Res. , vol.5 , pp. 1888-1897
    • Chou, K.C.1    Shen, H.B.2
  • 21
    • 84870431038 scopus 로고    scopus 로고
    • CD-HIT: accelerated for clustering the next-generation sequencing data
    • Fu L., Niu B., Zhu Z., Wu S., Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012, 28:3150-3152.
    • (2012) Bioinformatics , vol.28 , pp. 3150-3152
    • Fu, L.1    Niu, B.2    Zhu, Z.3    Wu, S.4    Li, W.5
  • 22
    • 84876053736 scopus 로고    scopus 로고
    • IRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition
    • Chen W., Feng P.M., Lin H., Chou K.C. iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Nucleic Acids Res. 2013, 41:e68.
    • (2013) Nucleic Acids Res. , vol.41 , pp. e68
    • Chen, W.1    Feng, P.M.2    Lin, H.3    Chou, K.C.4
  • 23
    • 84896463976 scopus 로고    scopus 로고
    • INuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition
    • Guo S.H., Deng E.Z., Xu L.Q., Ding H., Lin H., Chen W., Chou K.C. iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. Bioinformatics 2014, 30:1522-1529.
    • (2014) Bioinformatics , vol.30 , pp. 1522-1529
    • Guo, S.H.1    Deng, E.Z.2    Xu, L.Q.3    Ding, H.4    Lin, H.5    Chen, W.6    Chou, K.C.7
  • 24
    • 84900463301 scopus 로고    scopus 로고
    • PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition
    • Chen W., Lei T.Y., Jin D.C., Lin H., Chou K.C. PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition. Anal. Biochem. 2014, 456:50-63.
    • (2014) Anal. Biochem. , vol.456 , pp. 50-63
    • Chen, W.1    Lei, T.Y.2    Jin, D.C.3    Lin, H.4    Chou, K.C.5
  • 25
    • 84899627202 scopus 로고    scopus 로고
    • Training-free atomistic prediction of nucleosome occupancy
    • Minary P., Levitt M. Training-free atomistic prediction of nucleosome occupancy. Proc. Natl. Acad. Sci. U. S. A. 2014, 111:6293-6298.
    • (2014) Proc. Natl. Acad. Sci. U. S. A. , vol.111 , pp. 6293-6298
    • Minary, P.1    Levitt, M.2
  • 26
    • 0032168436 scopus 로고    scopus 로고
    • Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena
    • Munteanu M.G., Vlahovicek K., Parthasarathy S., Simon I., Pongor S. Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena. Trends Biochem. Sci. 1998, 23:341-347.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 341-347
    • Munteanu, M.G.1    Vlahovicek, K.2    Parthasarathy, S.3    Simon, I.4    Pongor, S.5
  • 27
    • 0028624664 scopus 로고
    • Bending and curvature calculations in B-DNA
    • Goodsell D.S., Dickerson R.E. Bending and curvature calculations in B-DNA. Nucleic Acids Res. 1994, 22:5497-5503.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 5497-5503
    • Goodsell, D.S.1    Dickerson, R.E.2
  • 28
    • 0023001414 scopus 로고
    • Sequence periodicities in chicken nucleosome core DNA
    • Satchwell S.C., Drew H.R., Travers A.A. Sequence periodicities in chicken nucleosome core DNA. J. Mol. Biol. 1986, 191:659-675.
    • (1986) J. Mol. Biol. , vol.191 , pp. 659-675
    • Satchwell, S.C.1    Drew, H.R.2    Travers, A.A.3
  • 29
    • 36448982458 scopus 로고    scopus 로고
    • Naive Bayes for microRNA target predictions-machine learning for microRNA targets
    • Yousef M., Jung S., Kossenkov A.V., Showe L.C., Showe M.K. Naive Bayes for microRNA target predictions-machine learning for microRNA targets. Bioinformatics 2007, 23:2987-2992.
    • (2007) Bioinformatics , vol.23 , pp. 2987-2992
    • Yousef, M.1    Jung, S.2    Kossenkov, A.V.3    Showe, L.C.4    Showe, M.K.5
  • 30
    • 84884269845 scopus 로고    scopus 로고
    • Identification of antioxidants from sequence information using naive Bayes
    • Feng P.M., Lin H., Chen W. Identification of antioxidants from sequence information using naive Bayes. Comput. Math. Methods Med. 2013, 2013:567529.
    • (2013) Comput. Math. Methods Med. , vol.2013 , pp. 567529
    • Feng, P.M.1    Lin, H.2    Chen, W.3
  • 31
    • 84878657414 scopus 로고    scopus 로고
    • Naive Bayes classifier with feature selection to identify phage virion proteins
    • Feng P.M., Ding H., Chen W., Lin H. Naive Bayes classifier with feature selection to identify phage virion proteins. Comput. Math. Methods Med. 2013, 2013:530696.
    • (2013) Comput. Math. Methods Med. , vol.2013 , pp. 530696
    • Feng, P.M.1    Ding, H.2    Chen, W.3    Lin, H.4
  • 32
    • 84885112194 scopus 로고    scopus 로고
    • AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes
    • Lin H., Chen W., Ding H. AcalPred: a sequence-based tool for discriminating between acidic and alkaline enzymes. PLoS One 2013, 8:e75726.
    • (2013) PLoS One , vol.8 , pp. e75726
    • Lin, H.1    Chen, W.2    Ding, H.3
  • 33
    • 84878789801 scopus 로고    scopus 로고
    • Using over-represented tetrapeptides to predict protein submitochondria locations
    • Lin H., Chen W., Yuan L.F., Li Z.Q., Ding H. Using over-represented tetrapeptides to predict protein submitochondria locations. Acta Biotheor. 2013, 61:259-268.
    • (2013) Acta Biotheor. , vol.61 , pp. 259-268
    • Lin, H.1    Chen, W.2    Yuan, L.F.3    Li, Z.Q.4    Ding, H.5
  • 34
    • 77958151520 scopus 로고    scopus 로고
    • Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information
    • Chen W., Lin H. Prediction of midbody, centrosome and kinetochore proteins based on gene ontology information. Biochem. Biophys. Res. Commun. 2010, 401:382-384.
    • (2010) Biochem. Biophys. Res. Commun. , vol.401 , pp. 382-384
    • Chen, W.1    Lin, H.2
  • 35
    • 84862819754 scopus 로고    scopus 로고
    • Prediction of replication origins by calculating DNA structural properties
    • Chen W., Feng P., Lin H. Prediction of replication origins by calculating DNA structural properties. FEBS Lett. 2012, 586:934-938.
    • (2012) FEBS Lett. , vol.586 , pp. 934-938
    • Chen, W.1    Feng, P.2    Lin, H.3
  • 36
    • 79955564229 scopus 로고    scopus 로고
    • Prediction of GABAA receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine
    • Mohabatkar H., Mohammad Beigi M., Esmaeili A. Prediction of GABAA receptor proteins using the concept of Chou's pseudo-amino acid composition and support vector machine. J. Theor. Biol. 2011, 281:18-23.
    • (2011) J. Theor. Biol. , vol.281 , pp. 18-23
    • Mohabatkar, H.1    Mohammad Beigi, M.2    Esmaeili, A.3
  • 37
    • 52149087297 scopus 로고    scopus 로고
    • Predicting membrane protein types by the LLDA algorithm
    • Wang T., Yang J., Shen H.B., Chou K.C. Predicting membrane protein types by the LLDA algorithm. Protein Pept. Lett. 2008, 15:915-921.
    • (2008) Protein Pept. Lett. , vol.15 , pp. 915-921
    • Wang, T.1    Yang, J.2    Shen, H.B.3    Chou, K.C.4


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