메뉴 건너뛰기




Volumn 260, Issue 1, 2009, Pages 104-109

Classification analysis of dual nucleotides using dimension reduction

Author keywords

Dual nucleotides compositions; Eubacteria; Genome; Graphic representation; Principal components analysis (PCA)

Indexed keywords

NUCLEOTIDE;

EID: 67949117109     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.05.011     Document Type: Article
Times cited : (8)

References (49)
  • 4
    • 42149097173 scopus 로고    scopus 로고
    • Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs
    • Andraos J. Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs. Canadian Journal of Chemistry 86 (2008) 342-357
    • (2008) Canadian Journal of Chemistry , vol.86 , pp. 342-357
    • Andraos, J.1
  • 5
    • 0019250029 scopus 로고
    • A new schematic method in enzyme kinetics
    • Chou K.C. A new schematic method in enzyme kinetics. European Journal of Biochemistry 113 (1980) 195-198
    • (1980) European Journal of Biochemistry , vol.113 , pp. 195-198
    • Chou, K.C.1
  • 6
    • 0024971003 scopus 로고
    • Graphical rules in steady and non-steady enzyme kinetics
    • Chou K.C. Graphical rules in steady and non-steady enzyme kinetics. Journal of Biological Chemistry 264 (1989) 12074-12079
    • (1989) Journal of Biological Chemistry , vol.264 , pp. 12074-12079
    • Chou, K.C.1
  • 7
    • 0025021607 scopus 로고
    • Review: applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems
    • Chou K.C. Review: applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems. Biophysical Chemistry 35 (1990) 1-24
    • (1990) Biophysical Chemistry , vol.35 , pp. 1-24
    • Chou, K.C.1
  • 8
    • 34250077148 scopus 로고
    • Graphic rule for non-steady-state enzyme kinetics and protein folding kinetics
    • Chou K.C. Graphic rule for non-steady-state enzyme kinetics and protein folding kinetics. Journal of Mathematical Chemistry 12 (1993) 97-108
    • (1993) Journal of Mathematical Chemistry , vol.12 , pp. 97-108
    • Chou, K.C.1
  • 9
    • 0032940342 scopus 로고    scopus 로고
    • Protein subcellular location prediction
    • Chou K.C., and Elrod D.W. Protein subcellular location prediction. Protein Engineering 12 (1999) 107-118
    • (1999) Protein Engineering , vol.12 , pp. 107-118
    • Chou, K.C.1    Elrod, D.W.2
  • 10
    • 0019021450 scopus 로고
    • Graphical rules for enzyme-catalyzed rate laws
    • Chou K.C., and Forsen S. Graphical rules for enzyme-catalyzed rate laws. Biochemical Journal 187 (1980) 829-835
    • (1980) Biochemical Journal , vol.187 , pp. 829-835
    • Chou, K.C.1    Forsen, S.2
  • 11
    • 0343751815 scopus 로고
    • Graphical rules of steady-state reaction systems
    • Chou K.C., and Forsen S. Graphical rules of steady-state reaction systems. Canadian Journal of Chemistry 59 (1981) 737-755
    • (1981) Canadian Journal of Chemistry , vol.59 , pp. 737-755
    • Chou, K.C.1    Forsen, S.2
  • 12
    • 0343315943 scopus 로고
    • Graph theory of enzyme kinetics: 1. Steady-state reaction system
    • Chou K.C., Jiang S.P., Liu W.M., and Fee C.H. Graph theory of enzyme kinetics: 1. Steady-state reaction system. Scientia Sinica 22 (1979) 341-358
    • (1979) Scientia Sinica , vol.22 , pp. 341-358
    • Chou, K.C.1    Jiang, S.P.2    Liu, W.M.3    Fee, C.H.4
  • 13
    • 0028071544 scopus 로고
    • Review: steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases
    • Chou K.C., Kezdy F.J., and Reusser F. Review: steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Analytical Biochemistry 221 (1994) 217-230
    • (1994) Analytical Biochemistry , vol.221 , pp. 217-230
    • Chou, K.C.1    Kezdy, F.J.2    Reusser, F.3
  • 14
    • 0019413602 scopus 로고
    • Graphical rules for non-steady state enzyme kinetics
    • Chou K.C., and Liu W.M. Graphical rules for non-steady state enzyme kinetics. Journal of Theoretical Biology 91 (1981) 637-654
    • (1981) Journal of Theoretical Biology , vol.91 , pp. 637-654
    • Chou, K.C.1    Liu, W.M.2
  • 15
    • 0027054450 scopus 로고
    • Diagrammatization of codon usage in 339 HIV proteins and its biological implication
    • Chou K.C., and Zhang C.T. Diagrammatization of codon usage in 339 HIV proteins and its biological implication. AIDS Research and Human Retroviruses 8 (1992) 1967-1976
    • (1992) AIDS Research and Human Retroviruses , vol.8 , pp. 1967-1976
    • Chou, K.C.1    Zhang, C.T.2
  • 18
    • 55549132598 scopus 로고    scopus 로고
    • Principal component analysis and quantitative image analysis to predict effects of toxics in anaerobic granular sludge
    • Costa J.C., Alves M.M., and Ferreira E.C. Principal component analysis and quantitative image analysis to predict effects of toxics in anaerobic granular sludge. Bioresource Technology 100 (2009) 1180-1185
    • (2009) Bioresource Technology , vol.100 , pp. 1180-1185
    • Costa, J.C.1    Alves, M.M.2    Ferreira, E.C.3
  • 19
  • 20
    • 33646568767 scopus 로고    scopus 로고
    • Amino acid principal component analysis (AAPCA) and its applications in protein structural class prediction
    • Du Q.S., Jiang Z.Q., He W.Z., Li D.P., and Chou K.C. Amino acid principal component analysis (AAPCA) and its applications in protein structural class prediction. Journal of Biomolecular Structure and Dynamics 23 (2006) 635-640
    • (2006) Journal of Biomolecular Structure and Dynamics , vol.23 , pp. 635-640
    • Du, Q.S.1    Jiang, Z.Q.2    He, W.Z.3    Li, D.P.4    Chou, K.C.5
  • 23
    • 33947472850 scopus 로고
    • A schematic method of deriving the rate laws for enzyme-catalyzed reactions
    • King E.L., and Altman C. A schematic method of deriving the rate laws for enzyme-catalyzed reactions. Journal of Physical Chemistry 60 (1956) 1375-1378
    • (1956) Journal of Physical Chemistry , vol.60 , pp. 1375-1378
    • King, E.L.1    Altman, C.2
  • 24
    • 0026503888 scopus 로고
    • Mixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation
    • Kuzmic P., Ng K.Y., and Heath T.D. Mixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation. Analytical Biochemistry 200 (1992) 68-73
    • (1992) Analytical Biochemistry , vol.200 , pp. 68-73
    • Kuzmic, P.1    Ng, K.Y.2    Heath, T.D.3
  • 25
    • 0025285220 scopus 로고
    • Demonstration of a slow conformational change in liver glucokinase by fluorescence spectroscopy
    • Lin S.X., and Neet K.E. Demonstration of a slow conformational change in liver glucokinase by fluorescence spectroscopy. Journal of Biological Chemistry 265 (1990) 9670-9675
    • (1990) Journal of Biological Chemistry , vol.265 , pp. 9670-9675
    • Lin, S.X.1    Neet, K.E.2
  • 26
    • 0021800102 scopus 로고
    • Microcomputer tools for steady-state enzyme kinetics
    • (original: Computer Applied Bioscience)
    • Myers D., and Palmer G. Microcomputer tools for steady-state enzyme kinetics. Bioinformatics 1 (1985) 105-110 (original: Computer Applied Bioscience)
    • (1985) Bioinformatics , vol.1 , pp. 105-110
    • Myers, D.1    Palmer, G.2
  • 27
    • 59449107136 scopus 로고    scopus 로고
    • Organisms can essentially be classified according to two codon patterns
    • Okayasu T., and Sorimachi K. Organisms can essentially be classified according to two codon patterns. Amino Acids 36 2 (2009) 261-271
    • (2009) Amino Acids , vol.36 , Issue.2 , pp. 261-271
    • Okayasu, T.1    Sorimachi, K.2
  • 28
    • 36249019849 scopus 로고    scopus 로고
    • New 3D graphical representation of DNA sequence based on dual nucleotides
    • Qi X.Q., Wen J., and Qi Z.H. New 3D graphical representation of DNA sequence based on dual nucleotides. Journal of Theoretical Biology 249 (2007) 681-690
    • (2007) Journal of Theoretical Biology , vol.249 , pp. 681-690
    • Qi, X.Q.1    Wen, J.2    Qi, Z.H.3
  • 29
    • 34247869892 scopus 로고    scopus 로고
    • Novel 2D graphical representation of DNA sequence based on dual nucleotides
    • Qi Z.H., and Qi X.Q. Novel 2D graphical representation of DNA sequence based on dual nucleotides. Chemical Physics Letters 440 (2007) 139-144
    • (2007) Chemical Physics Letters , vol.440 , pp. 139-144
    • Qi, Z.H.1    Qi, X.Q.2
  • 30
    • 34347358494 scopus 로고    scopus 로고
    • PN-curve: a 3D graphical representation of DNA sequences and their numerical characterization
    • Qi Z.H., and Fan T.R. PN-curve: a 3D graphical representation of DNA sequences and their numerical characterization. Chemical Physics Letters 442 (2007) 434-440
    • (2007) Chemical Physics Letters , vol.442 , pp. 434-440
    • Qi, Z.H.1    Fan, T.R.2
  • 31
    • 62749093652 scopus 로고    scopus 로고
    • Numerical characterization of DNA sequences based on digital signal method
    • Qi Z.H., and Qi X.Q. Numerical characterization of DNA sequences based on digital signal method. Computers in Biology and Medicine 39 (2009) 388-391
    • (2009) Computers in Biology and Medicine , vol.39 , pp. 388-391
    • Qi, Z.H.1    Qi, X.Q.2
  • 32
    • 34547106016 scopus 로고    scopus 로고
    • Multi-layered network structure of amino acid (AA) metabolism characterized by each essential AA-deficient condition
    • Shikata N., Maki Y., Noguchi Y., Mori M., Hanai T., Takahashi M., and Okamoto M. Multi-layered network structure of amino acid (AA) metabolism characterized by each essential AA-deficient condition. Amino Acids 33 (2007) 113-121
    • (2007) Amino Acids , vol.33 , pp. 113-121
    • Shikata, N.1    Maki, Y.2    Noguchi, Y.3    Mori, M.4    Hanai, T.5    Takahashi, M.6    Okamoto, M.7
  • 33
    • 67949111407 scopus 로고    scopus 로고
    • A proposed solution to the historic puzzle of Chargaff's second parity rule
    • Sorimachi K. A proposed solution to the historic puzzle of Chargaff's second parity rule. Open Genomics Journal 2 (2009) 12-14
    • (2009) Open Genomics Journal , vol.2 , pp. 12-14
    • Sorimachi, K.1
  • 34
    • 67949093159 scopus 로고    scopus 로고
    • Universal rules governing genome evolution expressed by linear formulas
    • Sorimachi K., and Okayasu T. Universal rules governing genome evolution expressed by linear formulas. Open Genomics Journal 1 (2008) 33-43
    • (2008) Open Genomics Journal , vol.1 , pp. 33-43
    • Sorimachi, K.1    Okayasu, T.2
  • 35
    • 2342578132 scopus 로고    scopus 로고
    • Classification of eubacteria based on their complete genome: where does Mycoplasmataceae belong?
    • Sorimachi K., and Okayasu T. Classification of eubacteria based on their complete genome: where does Mycoplasmataceae belong?. Biology Letters 271 (2004) S127-S130
    • (2004) Biology Letters , vol.271
    • Sorimachi, K.1    Okayasu, T.2
  • 36
    • 43149124638 scopus 로고    scopus 로고
    • Codon evolution is governed by linear formulas
    • Sorimachi K., and Okayasu T. Codon evolution is governed by linear formulas. Amino Acids 34 4 (2008) 661-668
    • (2008) Amino Acids , vol.34 , Issue.4 , pp. 661-668
    • Sorimachi, K.1    Okayasu, T.2
  • 38
  • 39
    • 15244357858 scopus 로고    scopus 로고
    • Using cellular automata to generate image representation for biological sequences
    • Xiao X., Shao S., Ding Y., Huang Z., Chen X., and Chou K.C. Using cellular automata to generate image representation for biological sequences. Amino Acids 28 (2005) 29-35
    • (2005) Amino Acids , vol.28 , pp. 29-35
    • Xiao, X.1    Shao, S.2    Ding, Y.3    Huang, Z.4    Chen, X.5    Chou, K.C.6
  • 40
    • 32944461574 scopus 로고    scopus 로고
    • Using cellular automata images and pseudo amino acid composition to predict protein subcellular location
    • Xiao X., Shao S.H., Ding Y.S., Huang Z.D., and Chou K.C. Using cellular automata images and pseudo amino acid composition to predict protein subcellular location. Amino Acids 30 (2006) 49-54
    • (2006) Amino Acids , vol.30 , pp. 49-54
    • Xiao, X.1    Shao, S.H.2    Ding, Y.S.3    Huang, Z.D.4    Chou, K.C.5
  • 41
    • 20344364176 scopus 로고    scopus 로고
    • An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation
    • Xiao X., Shao S., Ding Y., Huang Z., Chen X., and Chou K.C. An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation. Journal of Theoretical Biology 235 (2005) 555-565
    • (2005) Journal of Theoretical Biology , vol.235 , pp. 555-565
    • Xiao, X.1    Shao, S.2    Ding, Y.3    Huang, Z.4    Chen, X.5    Chou, K.C.6
  • 43
    • 51349105695 scopus 로고    scopus 로고
    • Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image
    • Xiao X., Wang P., and Chou K.C. Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image. Journal of Theoretical Biology 254 (2008) 691-696
    • (2008) Journal of Theoretical Biology , vol.254 , pp. 691-696
    • Xiao, X.1    Wang, P.2    Chou, K.C.3
  • 44
    • 64749096548 scopus 로고    scopus 로고
    • GPCR-CA: a cellular automaton image approach for predicting G-protein-coupled receptor functional classes
    • Xiao X., Wang P., and Chou K.C. GPCR-CA: a cellular automaton image approach for predicting G-protein-coupled receptor functional classes. Journal of Computational Chemistry 30 (2009) 1414-1423
    • (2009) Journal of Computational Chemistry , vol.30 , pp. 1414-1423
    • Xiao, X.1    Wang, P.2    Chou, K.C.3
  • 45
    • 33745141157 scopus 로고    scopus 로고
    • A new 2D graphical representation-classification curve and the analysis of similarity/dissimilarity of DNA sequences
    • Yao Y.H., Nan X.Y., and Wang T.M. A new 2D graphical representation-classification curve and the analysis of similarity/dissimilarity of DNA sequences. Journal of Molecular Structure: THEOCHEM 764 (2006) 101-108
    • (2006) Journal of Molecular Structure: THEOCHEM , vol.764 , pp. 101-108
    • Yao, Y.H.1    Nan, X.Y.2    Wang, T.M.3
  • 46
    • 0031558402 scopus 로고    scopus 로고
    • A symmetrical theory of DNA sequences and its applications
    • Zhang C.T. A symmetrical theory of DNA sequences and its applications. Journal of Theoretical Biology 187 (1997) 297-306
    • (1997) Journal of Theoretical Biology , vol.187 , pp. 297-306
    • Zhang, C.T.1
  • 47
    • 1242338884 scopus 로고    scopus 로고
    • Isochore structures in the mouse genome
    • Zhang C.T., and Zhang R. Isochore structures in the mouse genome. Genomics 83 (2004) 384-394
    • (2004) Genomics , vol.83 , pp. 384-394
    • Zhang, C.T.1    Zhang, R.2
  • 48
    • 0028237028 scopus 로고
    • Analysis of codon usage in 1562 E. coli protein coding sequences
    • Zhang C.T., and Chou K.C. Analysis of codon usage in 1562 E. coli protein coding sequences. Journal of Molecular Biology 238 (1994) 1-8
    • (1994) Journal of Molecular Biology , vol.238 , pp. 1-8
    • Zhang, C.T.1    Chou, K.C.2
  • 49
    • 0021764092 scopus 로고
    • An extension of Chou's graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways
    • Zhou G.P., and Deng M.H. An extension of Chou's graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways. Biochemical Journal 222 (1984) 169-176
    • (1984) Biochemical Journal , vol.222 , pp. 169-176
    • Zhou, G.P.1    Deng, M.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.