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Volumn 93, Issue 1, 2013, Pages 12-17

Database resources for the tuberculosis community

Author keywords

Database; Genomics; PATRIC; TB database; TubercuList

Indexed keywords

BACTERIAL GENOME; DATA BASE; DNA MODIFICATION; DNA SEQUENCE; GENE CONTROL; GENE EXPRESSION; GENOME ANALYSIS; HIGH THROUGHPUT SEQUENCING; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PIPELINE; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW; RNA ANALYSIS; RNA SEQUENCE; TUBERCULOSIS;

EID: 84874523447     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2012.11.003     Document Type: Review
Times cited : (24)

References (42)
  • 5
    • 0036774642 scopus 로고    scopus 로고
    • Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv
    • J.C. Camus, M.J. Pryor, C. Medigue, and S.T. Cole Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv Microbiology 148 2002 2967 2973
    • (2002) Microbiology , vol.148 , pp. 2967-2973
    • Camus, J.C.1    Pryor, M.J.2    Medigue, C.3    Cole, S.T.4
  • 6
  • 7
    • 84859165788 scopus 로고    scopus 로고
    • The genomes OnLine database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata
    • 10.1093/nar/gkr1100
    • I. Pagani, K. Liolios, J. Jansson, I.M. Chen, T. Smirnova, B. Nosrat, V.M. Markowitz, and N.C. Kyrpides The genomes OnLine database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata Nucleic Acid Res 40 2012 D571 D579 10.1093/nar/gkr1100
    • (2012) Nucleic Acid Res , vol.40
    • Pagani, I.1    Liolios, K.2    Jansson, J.3    Chen, I.M.4    Smirnova, T.5    Nosrat, B.6    Markowitz, V.M.7    Kyrpides, N.C.8
  • 9
    • 36949032098 scopus 로고    scopus 로고
    • Annotation, comparison and databases for hundreds of bacterial genomes
    • 10.1016/j.resmic.2007.09.009
    • C. Medigue, and I. Moszer Annotation, comparison and databases for hundreds of bacterial genomes Res Microbiol 158 2007 724 736 10.1016/j.resmic.2007.09.009
    • (2007) Res Microbiol , vol.158 , pp. 724-736
    • Medigue, C.1    Moszer, I.2
  • 10
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • 10.1093/nar/gkr981
    • U. Consortium Reorganizing the protein space at the Universal Protein Resource (UniProt) Nucleic Acid Res 40 2012 D71 D75 10.1093/nar/gkr981
    • (2012) Nucleic Acid Res , vol.40
    • Consortium, U.1
  • 11
    • 79955031171 scopus 로고    scopus 로고
    • AprABC: A Mycobacterium tuberculosis complex-specific locus that modulates pH-driven adaptation to the macrophage phagosome
    • 10.1111/j.1365-2958.2011.07601.x
    • R.B. Abramovitch, K.H. Rohde, F.F. Hsu, and D.G. Russell aprABC: a Mycobacterium tuberculosis complex-specific locus that modulates pH-driven adaptation to the macrophage phagosome Mol Microbiol 80 2011 678 694 10.1111/j.1365-2958.2011.07601.x
    • (2011) Mol Microbiol , vol.80 , pp. 678-694
    • Abramovitch, R.B.1    Rohde, K.H.2    Hsu, F.F.3    Russell, D.G.4
  • 12
    • 78651081719 scopus 로고    scopus 로고
    • Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners
    • 10.1186/1471-2164-12-21
    • D.H. Haft Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners BMC Genomics 12 2011 21 10.1186/1471-2164-12-21
    • (2011) BMC Genomics , vol.12 , pp. 21
    • Haft, D.H.1
  • 13
    • 84860731440 scopus 로고    scopus 로고
    • Non-coding RNA and its potential role in Mycobacterium tuberculosis pathogenesis
    • K. Arnvig, and D. Young Non-coding RNA and its potential role in Mycobacterium tuberculosis pathogenesis RNA Biol 9 2012
    • (2012) RNA Biol , vol.9
    • Arnvig, K.1    Young, D.2
  • 14
    • 77955077136 scopus 로고    scopus 로고
    • Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis
    • 10.1093/nar/gkq101
    • J.M. DiChiara, L.M. Contreras-Martinez, J. Livny, D. Smith, K.A. McDonough, and M. Belfort Multiple small RNAs identified in Mycobacterium bovis BCG are also expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis Nucleic Acid Res 38 2010 4067 4078 10.1093/nar/gkq101
    • (2010) Nucleic Acid Res , vol.38 , pp. 4067-4078
    • Dichiara, J.M.1    Contreras-Martinez, L.M.2    Livny, J.3    Smith, D.4    McDonough, K.A.5    Belfort, M.6
  • 15
    • 79960461488 scopus 로고    scopus 로고
    • A proteomic view of mycobacteria
    • 10.1002/pmic.201100043
    • G.A. de Souza, and H.G. Wiker A proteomic view of mycobacteria Proteomics 11 2011 3118 3127 10.1002/pmic.201100043
    • (2011) Proteomics , vol.11 , pp. 3118-3127
    • De Souza, G.A.1    Wiker, H.G.2
  • 16
    • 84855521821 scopus 로고    scopus 로고
    • Prospective on Mycobacterium tuberculosis proteomics
    • 10.1021/pr2008658
    • M.C. Mehaffy, N.A. Kruh-Garcia, and K.M. Dobos Prospective on Mycobacterium tuberculosis proteomics J Proteome Res 11 2012 17 25 10.1021/pr2008658
    • (2012) J Proteome Res , vol.11 , pp. 17-25
    • Mehaffy, M.C.1    Kruh-Garcia, N.A.2    Dobos, K.M.3
  • 17
    • 79551475673 scopus 로고    scopus 로고
    • Proteogenomics
    • 10.1002/pmic.201000615
    • S. Renuse, R. Chaerkady, and A. Pandey Proteogenomics Proteomics 11 2011 620 630 10.1002/pmic.201000615
    • (2011) Proteomics , vol.11 , pp. 620-630
    • Renuse, S.1    Chaerkady, R.2    Pandey, A.3
  • 19
    • 79960430601 scopus 로고    scopus 로고
    • The progress made in determining the Mycobacterium tuberculosis structural proteome
    • 10.1002/pmic.201000787
    • M.T. Ehebauer, and M. Wilmanns The progress made in determining the Mycobacterium tuberculosis structural proteome Proteomics 11 2011 3128 3133 10.1002/pmic.201000787
    • (2011) Proteomics , vol.11 , pp. 3128-3133
    • Ehebauer, M.T.1    Wilmanns, M.2
  • 20
    • 77949360269 scopus 로고    scopus 로고
    • Template-based protein modeling: Recent methodological advances
    • P.R. Daga, R.Y. Patel, and R.J. Doerksen Template-based protein modeling: recent methodological advances Curr Top Med Chem 10 2010 84 94
    • (2010) Curr Top Med Chem , vol.10 , pp. 84-94
    • Daga, P.R.1    Patel, R.Y.2    Doerksen, R.J.3
  • 21
    • 33748774384 scopus 로고    scopus 로고
    • Regulation of the expression of whiB1 in Mycobacterium tuberculosis: Role of cAMP receptor protein
    • 10.1099/mic.0.28924-0
    • N. Agarwal, T.R. Raghunand, and W.R. Bishai Regulation of the expression of whiB1 in Mycobacterium tuberculosis: role of cAMP receptor protein Microbiology 152 2006 2749 2756 10.1099/mic.0.28924-0
    • (2006) Microbiology , vol.152 , pp. 2749-2756
    • Agarwal, N.1    Raghunand, T.R.2    Bishai, W.R.3
  • 22
    • 35648975285 scopus 로고    scopus 로고
    • The Mycobacterium bovis BCG cyclic AMP receptor-like protein is a functional DNA binding protein in vitro and in vivo, but its activity differs from that of its M. tuberculosis ortholog, Rv3676
    • 10.1128/IAI.00658-07
    • G. Bai, M.A. Gazdik, D.D. Schaak, and K.A. McDonough The Mycobacterium bovis BCG cyclic AMP receptor-like protein is a functional DNA binding protein in vitro and in vivo, but its activity differs from that of its M. tuberculosis ortholog, Rv3676 Infect Immun 75 2007 5509 5517 10.1128/IAI.00658-07
    • (2007) Infect Immun , vol.75 , pp. 5509-5517
    • Bai, G.1    Gazdik, M.A.2    Schaak, D.D.3    McDonough, K.A.4
  • 23
    • 77954579484 scopus 로고    scopus 로고
    • Characterization of the transcriptional regulator Rv3124 of Mycobacterium tuberculosis identifies it as a positive regulator of molybdopterin biosynthesis and defines the functional consequences of a non-synonymous SNP in the Mycobacterium bovis BCG orthologue
    • 10.1099/mic.0.037200-0
    • P. Mendoza Lopez, P. Golby, E. Wooff, J. Nunez Garcia, M.C. Garcia Pelayo, K. Conlon, A. Gema Camacho, R.G. Hewinson, J. Polaina, A. Suarez Garcia, and S.V. Gordon Characterization of the transcriptional regulator Rv3124 of Mycobacterium tuberculosis identifies it as a positive regulator of molybdopterin biosynthesis and defines the functional consequences of a non-synonymous SNP in the Mycobacterium bovis BCG orthologue Microbiology 156 2010 2112 2123 10.1099/mic.0.037200-0
    • (2010) Microbiology , vol.156 , pp. 2112-2123
    • Mendoza Lopez, P.1    Golby, P.2    Wooff, E.3    Nunez Garcia, J.4    Garcia Pelayo, M.C.5    Conlon, K.6    Gema Camacho, A.7    Hewinson, R.G.8    Polaina, J.9    Suarez Garcia, A.10    Gordon, S.V.11
  • 24
    • 34247245826 scopus 로고    scopus 로고
    • Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis
    • 10.1099/mic.0.29281-0
    • X. Pang, P. Vu, T.F. Byrd, S. Ghanny, P. Soteropoulos, G.V. Mukamolova, S. Wu, B. Samten, and S.T. Howard Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis Microbiology 153 2007 1229 1242 10.1099/mic.0.29281-0
    • (2007) Microbiology , vol.153 , pp. 1229-1242
    • Pang, X.1    Vu, P.2    Byrd, T.F.3    Ghanny, S.4    Soteropoulos, P.5    Mukamolova, G.V.6    Wu, S.7    Samten, B.8    Howard, S.T.9
  • 25
    • 33947415761 scopus 로고    scopus 로고
    • Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays
    • 10.1128/JB.01371-06
    • S. Rodrigue, J. Brodeur, P.E. Jacques, A.L. Gervais, R. Brzezinski, and L. Gaudreau Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays J Bacteriol 189 2007 1505 1513 10.1128/JB.01371-06
    • (2007) J Bacteriol , vol.189 , pp. 1505-1513
    • Rodrigue, S.1    Brodeur, J.2    Jacques, P.E.3    Gervais, A.L.4    Brzezinski, R.5    Gaudreau, L.6
  • 26
    • 40549105136 scopus 로고    scopus 로고
    • Evolution of the mycobacterial SigK regulon
    • 10.1128/JB.01452-07
    • F. Veyrier, B. Said-Salim, and M.A. Behr Evolution of the mycobacterial SigK regulon J Bacteriol 190 2008 1891 1899 10.1128/JB.01452-07
    • (2008) J Bacteriol , vol.190 , pp. 1891-1899
    • Veyrier, F.1    Said-Salim, B.2    Behr, M.A.3
  • 29
    • 44349115626 scopus 로고    scopus 로고
    • Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: Antigenicity and genetic regulation
    • 10.1099/mic.0.2007/014548-0
    • P. Golby, J. Nunez, P.J. Cockle, K. Ewer, K. Logan, P. Hogarth, H.M. Vordermeier, J. Hinds, R.G. Hewinson, and S.V. Gordon Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation Microbiology 154 2008 1059 1067 10.1099/mic.0.2007/014548-0
    • (2008) Microbiology , vol.154 , pp. 1059-1067
    • Golby, P.1    Nunez, J.2    Cockle, P.J.3    Ewer, K.4    Logan, K.5    Hogarth, P.6    Vordermeier, H.M.7    Hinds, J.8    Hewinson, R.G.9    Gordon, S.V.10
  • 30
    • 78651088622 scopus 로고    scopus 로고
    • Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database
    • 10.1074/mcp.M110.002527 M110 002527
    • G.A. de Souza, M.O. Arntzen, S. Fortuin, A.C. Schurch, H. Malen, C.R. McEvoy, D. van Soolingen, B. Thiede, R.M. Warren, and H.G. Wiker Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database Mol Cell Prot 10 2011 10.1074/mcp.M110.002527 M110 002527
    • (2011) Mol Cell Prot , vol.10
    • De Souza, G.A.1    Arntzen, M.O.2    Fortuin, S.3    Schurch, A.C.4    Malen, H.5    McEvoy, C.R.6    Van Soolingen, D.7    Thiede, B.8    Warren, R.M.9    Wiker, H.G.10
  • 32
    • 84860349834 scopus 로고    scopus 로고
    • A screen for non-coding RNA in Mycobacterium tuberculosis reveals a cAMP-responsive RNA that is expressed during infection
    • 10.1016/j.gene.2012.03.044
    • S. Pelly, W.R. Bishai, and G. Lamichhane A screen for non-coding RNA in Mycobacterium tuberculosis reveals a cAMP-responsive RNA that is expressed during infection Gene 500 2012 85 92 10.1016/j.gene.2012.03.044
    • (2012) Gene , vol.500 , pp. 85-92
    • Pelly, S.1    Bishai, W.R.2    Lamichhane, G.3
  • 35
    • 84862492836 scopus 로고    scopus 로고
    • Function prediction and analysis of Mycobacterium tuberculosis hypothetical proteins
    • 10.3390/ijms13067283
    • G.K. Mazandu, and N.J. Mulder Function prediction and analysis of Mycobacterium tuberculosis hypothetical proteins Int J Mol Sci 13 2012 7283 7302 10.3390/ijms13067283
    • (2012) Int J Mol Sci , vol.13 , pp. 7283-7302
    • Mazandu, G.K.1    Mulder, N.J.2
  • 41
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • 10.1186/gb-2010-11-8-r86
    • J. Goecks, A. Nekrutenko, and J. Taylor Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol 11 2010 R86 10.1186/gb-2010-11-8-r86
    • (2010) Genome Biol , vol.11 , pp. 86
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3
  • 42
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • M. Kanehisa, and S. Goto KEGG: kyoto encyclopedia of genes and genomes Nucleic Acid Res 28 2000 27 30
    • (2000) Nucleic Acid Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2


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