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Volumn 5, Issue , 2015, Pages

Evolutionary conservation analysis between the essential and nonessential genes in bacterial genomes

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

EID: 84939442818     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep13210     Document Type: Article
Times cited : (71)

References (28)
  • 1
    • 0345668475 scopus 로고    scopus 로고
    • Essential Bacillus subtilis genes
    • Kobayashi, K. et al. Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100, 4678-4683 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 4678-4683
    • Kobayashi, K.1
  • 2
    • 80053098802 scopus 로고    scopus 로고
    • Essence of life: Essential genes of minimal genomes
    • Juhas, M., Eberl, L. & Glass, J. I. Essence of life: essential genes of minimal genomes. Trends Cell Biol. 21, 562-568 (2011).
    • (2011) Trends Cell Biol. , vol.21 , pp. 562-568
    • Juhas, M.1    Eberl, L.2    Glass, J.I.3
  • 3
    • 84891786814 scopus 로고    scopus 로고
    • DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements
    • Luo, H., Lin, Y., Gao, F., Zhang, C. T. & Zhang, R. DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res. 42, D574-D580 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. D574-D580
    • Luo, H.1    Lin, Y.2    Gao, F.3    Zhang, C.T.4    Zhang, R.5
  • 4
    • 84905841461 scopus 로고    scopus 로고
    • Protein localization analysis of essential genes in prokaryotes
    • Peng, C. & Gao, F. Protein localization analysis of essential genes in prokaryotes. Sci Rep 4, 6001 (2014).
    • (2014) Sci Rep , vol.4 , pp. 6001
    • Peng, C.1    Gao, F.2
  • 5
    • 77952744822 scopus 로고    scopus 로고
    • Functionality of essential genes drives gene strand-bias in bacterial genomes
    • Lin, Y., Gao, F. & Zhang, C. T. Functionality of essential genes drives gene strand-bias in bacterial genomes. Biochem. Biophys. Res. Commun. 396, 472-476 (2010).
    • (2010) Biochem. Biophys. Res. Commun. , vol.396 , pp. 472-476
    • Lin, Y.1    Gao, F.2    Zhang, C.T.3
  • 6
    • 84939439321 scopus 로고    scopus 로고
    • Protein-protein Interaction Networks of E. Coli and S. Cerevisiae are similar
    • Wuchty, S. & Uetz, P. Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar. Sci Rep 4, 7187 (2014).
    • (2014) Sci Rep , vol.4 , pp. 7187
    • Wuchty, S.1    Uetz, P.2
  • 7
    • 79959574838 scopus 로고    scopus 로고
    • Enzymes are enriched in bacterial essential genes
    • Gao, F. & Zhang, R. R. Enzymes are enriched in bacterial essential genes. PLoS ONE 6, e21683 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e21683
    • Gao, F.1    Zhang, R.R.2
  • 8
    • 84860112417 scopus 로고    scopus 로고
    • Putative essential and core-essential genes in Mycoplasma genomes
    • Lin, Y. & Zhang, R. R. Putative essential and core-essential genes in Mycoplasma genomes. Sci Rep 1, 53 (2011).
    • (2011) Sci Rep , vol.1 , pp. 53
    • Lin, Y.1    Zhang, R.R.2
  • 9
    • 84881583820 scopus 로고    scopus 로고
    • Geptop: A gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny
    • Wei, W., Ning, L. W., Ye, Y. N. & Guo, F. B. Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny. PLoS ONE 8, e72343 (2013).
    • (2013) PLoS ONE , vol.8 , pp. e72343
    • Wei, W.1    Ning, L.W.2    Ye, Y.N.3    Guo, F.B.4
  • 10
    • 72949094885 scopus 로고    scopus 로고
    • Predicting essential genes based on network and sequence analysis
    • Hwang, Y. C. et al. Predicting essential genes based on network and sequence analysis. Mol. Biosyst. 5, 1672-1678 (2009).
    • (2009) Mol. Biosyst. , vol.5 , pp. 1672-1678
    • Hwang, Y.C.1
  • 11
    • 79951573994 scopus 로고    scopus 로고
    • Investigating the predictability of essential genes across distantly related organisms using an integrative approach
    • Deng, J. et al. Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res. 39, 795-807 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. 795-807
    • Deng, J.1
  • 12
    • 84867696427 scopus 로고    scopus 로고
    • Essential genes as antimicrobial targets and cornerstones of synthetic biology
    • Juhas, M., Eberl, L. & Church, G. M. Essential genes as antimicrobial targets and cornerstones of synthetic biology. Trends Biotechnol. 30, 601-607 (2012).
    • (2012) Trends Biotechnol. , vol.30 , pp. 601-607
    • Juhas, M.1    Eberl, L.2    Church, G.M.3
  • 13
    • 0027403961 scopus 로고
    • Unbiased estimation of the rates of synonymous and nonsynonymous substitution
    • Li, W. H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36, 96-99 (1993).
    • (1993) J. Mol. Evol. , vol.36 , pp. 96-99
    • Li, W.H.1
  • 14
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • Jordan, I. K., Rogozin, I. B., Wolf, Y. I. & Koonin, E. V. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12, 962-968 (2002).
    • (2002) Genome Res. , vol.12 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 15
    • 84880911139 scopus 로고    scopus 로고
    • Transcriptional abundance is not the single force driving the evolution of bacterial proteins
    • Wei, W., Zhang, T., Lin, D., Yang, Z. J. & Guo, F. B. Transcriptional abundance is not the single force driving the evolution of bacterial proteins. BMC Evol. Biol. 13, 162 (2013).
    • (2013) BMC Evol. Biol. , vol.13 , pp. 162
    • Wei, W.1    Zhang, T.2    Lin, D.3    Yang, Z.J.4    Guo, F.B.5
  • 16
    • 58149197597 scopus 로고    scopus 로고
    • DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
    • Zhang, R. & Lin, Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 37, D455-D458 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. D455-D458
    • Zhang, R.1    Lin, Y.2
  • 17
    • 0346494858 scopus 로고    scopus 로고
    • DEG: A database of essential genes
    • Zhang, R., Ou, H. Y. & Zhang, C. T. DEG: a database of essential genes. Nucleic Acids Res. 32, D271-272 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. D271-272
    • Zhang, R.1    Ou, H.Y.2    Zhang, C.T.3
  • 18
    • 0036720020 scopus 로고    scopus 로고
    • The Ka/Ks ratio: Diagnosing the form of sequence evolution
    • Hurst, L. D. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18, 486 (2002).
    • (2002) Trends Genet. , vol.18 , pp. 486
    • Hurst, L.D.1
  • 19
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+ : Architecture and applications
    • Camacho, C. et al. BLAST+ : architecture and applications. BMC Bioinformatics 10, 421 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 20
    • 33747847779 scopus 로고    scopus 로고
    • PAL2NAL: Robust conversion of protein sequence alignments into the corresponding codon alignments
    • Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609-W612 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. W609-W612
    • Suyama, M.1    Torrents, D.2    Bork, P.3
  • 21
    • 36448991500 scopus 로고    scopus 로고
    • Clustal W and Clustal X version 2.0
    • Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.A.1
  • 22
    • 34248669040 scopus 로고    scopus 로고
    • KaKs-Calculator: Calculating Ka and Ks through model selection and model averaging
    • Zhang, Z. et al. KaKs-Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 4, 259-263 (2006).
    • (2006) Genomics Proteomics Bioinformatics , vol.4 , pp. 259-263
    • Zhang, Z.1
  • 23
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418-426 (1986).
    • (1986) Mol. Biol. Evol. , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 24
    • 84941067064 scopus 로고    scopus 로고
    • Expanded microbial genome coverage and improved protein family annotation in the COG database
    • Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261-269 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. D261-D269
    • Galperin, M.Y.1    Makarova, K.S.2    Wolf, Y.I.3    Koonin, E.V.4
  • 25
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: Freely available Python tools for computational molecular biology and bioinformatics
    • Cock, P. J. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25, 1422-1423 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.1
  • 26
    • 84876566990 scopus 로고    scopus 로고
    • DoriC 5.0: An updated database of oriC regions in both bacterial and archaeal genomes
    • Gao, F., Luo, H. & Zhang, C. T. DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Res. 41, D90-93 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. D90-93
    • Gao, F.1    Luo, H.2    Zhang, C.T.3
  • 27
    • 77950678110 scopus 로고    scopus 로고
    • Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa
    • Dotsch, A. et al. Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa. BMC Genomics 11, 234 (2010).
    • (2010) BMC Genomics , vol.11 , pp. 234
    • Dotsch, A.1
  • 28
    • 26444558214 scopus 로고    scopus 로고
    • How essential are nonessential genes?
    • Fang, G., Rocha, E. & Danchin, A. How essential are nonessential genes? Mol. Biol. Evol. 22, 2147-2156 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 2147-2156
    • Fang, G.1    Rocha, E.2    Danchin, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.