메뉴 건너뛰기




Volumn 9, Issue , 2008, Pages

A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; BACTERIAL STRAIN; CANCER CELL CULTURE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DATA ANALYSIS; ESCHERICHIA COLI; GENE IDENTIFICATION; GENETIC VARIABILITY; GENOME ANALYSIS; KERNEL METHOD; MICROARRAY ANALYSIS; NONHUMAN; REFERENCE VALUE; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS; ALGORITHM; CLASSIFICATION; COMPARATIVE STUDY; DNA MICROARRAY; ESCHERICHIA COLI K 12; ESCHERICHIA COLI O157; EVALUATION; GENE DOSAGE; GENETICS; GENOMICS; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; SPECIES DIFFERENCE; STATISTICAL ANALYSIS; STATISTICAL MODEL; STATISTICS;

EID: 40449142434     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-53     Document Type: Article
Times cited : (21)

References (54)
  • 1
    • 0036051847 scopus 로고    scopus 로고
    • Microarray analysis of bacterial pathogenicity
    • 12073651
    • Schoolnik GK Microarray analysis of bacterial pathogenicity Adv Microb Physiol 2002, 46:1-45 12073651
    • (2002) Adv Microb Physiol , vol.46 , pp. 1-45
    • Schoolnik, G.K.1
  • 3
    • 20044375763 scopus 로고    scopus 로고
    • Array comparative genomic hybridization and its applications in cancer
    • 10.1038/ng1569 15920524
    • Pinkel D Albertson DG Array comparative genomic hybridization and its applications in cancer Nat Genet 2005 37(Suppl):S11-7 10.1038/ng1569 15920524
    • (2005) Nat Genet , vol.37 , Issue.SUPPL.
    • Pinkel, D.1    Albertson, D.G.2
  • 4
    • 17344371740 scopus 로고    scopus 로고
    • High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
    • 10.1038/2524 9771718
    • Pinkel D Segraves R Sudar D Clark S Poole I Kowbel D Collins C Kuo WL Chen C Zhai Y High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays Nat Genet 1998, 20:207-11 10.1038/2524 9771718
    • (1998) Nat Genet , vol.20 , pp. 207-211
    • Pinkel, D.1    Segraves, R.2    Sudar, D.3    Clark, S.4    Poole, I.5    Kowbel, D.6    Collins, C.7    Kuo, W.L.8    Chen, C.9    Zhai, Y.10
  • 7
    • 27544483495 scopus 로고    scopus 로고
    • Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data
    • 10.1093/bioinformatics/bti611 16081473
    • Lai WR Johnson MD Kucherlapati R Park PJ Comparative analysis of algorithms for identifying amplifications and deletions in array CGH data Bioinformatics 2005, 21:3763-70 10.1093/bioinformatics/bti611 16081473
    • (2005) Bioinformatics , vol.21 , pp. 3763-3770
    • Lai, W.R.1    Johnson, M.D.2    Kucherlapati, R.3    Park, P.J.4
  • 8
    • 33744953369 scopus 로고    scopus 로고
    • Computational Methods for the Analysis of Array Comparative Genomic Hybridization
    • 2067254 17992253
    • Chari R Lockwood WW Lam WL Computational Methods for the Analysis of Array Comparative Genomic Hybridization Cancer Inform 2006, 2:48-58 2067254 17992253
    • (2006) Cancer Inform , vol.2 , pp. 48-58
    • Chari, R.1    Lockwood, W.W.2    Lam, W.L.3
  • 9
    • 22844435668 scopus 로고    scopus 로고
    • CGHPRO - A comprehensive data analysis tool for array CGH
    • 1274268 15807904 10.1186/1471-2105-6-85
    • Chen W Erdogan F Ropers HH Lenzner S Ullmann R CGHPRO - a comprehensive data analysis tool for array CGH BMC Bioinformatics 2005, 6:85 1274268 15807904 10.1186/1471-2105-6-85
    • (2005) BMC Bioinformatics , vol.6 , pp. 85
    • Chen, W.1    Erdogan, F.2    Ropers, H.H.3    Lenzner, S.4    Ullmann, R.5
  • 10
    • 34247181241 scopus 로고    scopus 로고
    • Exploiting noise in array CGH data to improve detection of DNA copy number change
    • 1994778 17272296 10.1093/nar/gkl730
    • Hu J Gao JB Cao Y Bottinger E Zhang W Exploiting noise in array CGH data to improve detection of DNA copy number change Nucleic Acids Res 2007, 35:e35 1994778 17272296 10.1093/nar/gkl730
    • (2007) Nucleic Acids Res , vol.35
    • Hu, J.1    Gao, J.B.2    Cao, Y.3    Bottinger, E.4    Zhang, W.5
  • 11
    • 34547547951 scopus 로고    scopus 로고
    • Double trouble: Medical implications of genetic duplication and amplification in bacteria
    • 10.2217/17460913.2.3.309 17661705
    • Craven SH Neidle EL Double trouble: Medical implications of genetic duplication and amplification in bacteria Future Microbiol 2007, 2:309-21 10.2217/17460913.2.3.309 17661705
    • (2007) Future Microbiol , vol.2 , pp. 309-321
    • Craven, S.H.1    Neidle, E.L.2
  • 12
    • 0033776631 scopus 로고    scopus 로고
    • Genome rearrangement by replication-directed translocation
    • 10.1038/79918 11017076
    • Tillier ER Collins RA Genome rearrangement by replication-directed translocation Nat Genet 2000, 26:195-7 10.1038/79918 11017076
    • (2000) Nat Genet , vol.26 , pp. 195-197
    • Tillier, E.R.1    Collins, R.A.2
  • 13
    • 0026490002 scopus 로고
    • Evolution by acquisition: The case for horizontal gene transfers
    • 10.1016/0968-0004(92)90335-7 1471257
    • Smith MW Feng DF Doolittle RF Evolution by acquisition: The case for horizontal gene transfers Trends Biochem Sci 1992, 17:489-93 10.1016/ 0968-0004(92)90335-7 1471257
    • (1992) Trends Biochem Sci , vol.17 , pp. 489-493
    • Smith, M.W.1    Feng, D.F.2    Doolittle, R.F.3
  • 14
    • 23944475626 scopus 로고    scopus 로고
    • Mechanisms of, and barriers to, horizontal gene transfer between bacteria
    • 10.1038/nrmicro1234 16138099
    • Thomas CM Nielsen KM Mechanisms of, and barriers to, horizontal gene transfer between bacteria Nat Rev Microbiol 2005, 3:711-21 10.1038/ nrmicro1234 16138099
    • (2005) Nat Rev Microbiol , vol.3 , pp. 711-721
    • Thomas, C.M.1    Nielsen, K.M.2
  • 16
    • 0036595304 scopus 로고    scopus 로고
    • Horizontal gene transfer in microbial genome evolution
    • 10.1006/tpbi.2002.1596 12167368
    • Jain R Rivera MC Moore JE Lake JA Horizontal gene transfer in microbial genome evolution Theor Popul Biol 2002, 61:489-95 10.1006/tpbi.2002.1596 12167368
    • (2002) Theor Popul Biol , vol.61 , pp. 489-495
    • Jain, R.1    Rivera, M.C.2    Moore, J.E.3    Lake, J.A.4
  • 17
    • 0242371471 scopus 로고    scopus 로고
    • Horizontal gene transfer accelerates genome innovation and evolution
    • 10.1093/molbev/msg154 12777514
    • Jain R Rivera MC Moore JE Lake JA Horizontal gene transfer accelerates genome innovation and evolution Mol Biol Evol 2003, 20:1598-602 10.1093/ molbev/msg154 12777514
    • (2003) Mol Biol Evol , vol.20 , pp. 1598-1602
    • Jain, R.1    Rivera, M.C.2    Moore, J.E.3    Lake, J.A.4
  • 18
    • 0034671796 scopus 로고    scopus 로고
    • Evolutionary dynamics of full genome content in Escherichia coli
    • 305890 11118198 10.1093/emboj/19.24.6637
    • Ochman H Jones IB Evolutionary dynamics of full genome content in Escherichia coli Embo J 2000, 19:6637-43 305890 11118198 10.1093/emboj/ 19.24.6637
    • (2000) Embo J , vol.19 , pp. 6637-6643
    • Ochman, H.1    Jones, I.B.2
  • 19
    • 0037173117 scopus 로고    scopus 로고
    • Evolutionary genomics of Salmonella: Gene acquisitions revealed by microarray analysis
    • 124405 12072558 10.1073/pnas.122153699
    • Porwollik S Wong RM McClelland M Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis Proc Natl Acad Sci USA 2002, 99:8956-61 124405 12072558 10.1073/pnas.122153699
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8956-8961
    • Porwollik, S.1    Wong, R.M.2    McClelland, M.3
  • 20
    • 0037224655 scopus 로고    scopus 로고
    • Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray
    • 145314 12511502 10.1128/JB.185.2.553-563.2003
    • Chan K Baker S Kim CC Detweiler CS Dougan G Falkow S Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray J Bacteriol 2003, 185:553-63 145314 12511502 10.1128/JB.185.2.553-563.2003
    • (2003) J Bacteriol , vol.185 , pp. 553-563
    • Chan, K.1    Baker, S.2    Kim, C.C.3    Detweiler, C.S.4    Dougan, G.5    Falkow, S.6
  • 21
    • 28444474563 scopus 로고    scopus 로고
    • Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray
    • 1307019 16299280 10.1128/IAI.73.12.7894-7905.2005
    • Anjum MF Marooney C Fookes M Baker S Dougan G Ivens A Woodward MJ Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray Infect Immun 2005, 73:7894-905 1307019 16299280 10.1128/IAI.73.12.7894-7905.2005
    • (2005) Infect Immun , vol.73 , pp. 7894-7905
    • Anjum, M.F.1    Marooney, C.2    Fookes, M.3    Baker, S.4    Dougan, G.5    Ivens, A.6    Woodward, M.J.7
  • 22
    • 0042766188 scopus 로고    scopus 로고
    • Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens
    • 165989 12874348 10.1128/IAI.71.8.4674-4683.2003
    • Anjum MF Lucchini S Thompson A Hinton JC Woodward MJ Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens Infect Immun 2003, 71:4674-83 165989 12874348 10.1128/IAI.71.8.4674-4683.2003
    • (2003) Infect Immun , vol.71 , pp. 4674-4683
    • Anjum, M.F.1    Lucchini, S.2    Thompson, A.3    Hinton, J.C.4    Woodward, M.J.5
  • 23
    • 33646569143 scopus 로고    scopus 로고
    • Detecting genetic variability among different Mycobacterium tuberculosis strains using DNA microarrays technology
    • 10.1016/j.tube.2006.01.002 16644284
    • Diaz R Siddiqi N Rubin EJ Detecting genetic variability among different Mycobacterium tuberculosis strains using DNA microarrays technology Tuberculosis (Edinb) 2006, 86:314-8 10.1016/j.tube.2006.01.002 16644284
    • (2006) Tuberculosis (Edinb) , vol.86 , pp. 314-318
    • Diaz, R.1    Siddiqi, N.2    Rubin, E.J.3
  • 24
    • 2942571207 scopus 로고    scopus 로고
    • Extensive genomic diversity in pathogenic Escherichia coli and Shigella Strains revealed by comparative genomic hybridization microarray
    • 419953 15175305 10.1128/JB.186.12.3911-3921.2004
    • Fukiya S Mizoguchi H Tobe T Mori H Extensive genomic diversity in pathogenic Escherichia coli and Shigella Strains revealed by comparative genomic hybridization microarray J Bacteriol 2004, 186:3911-21 419953 15175305 10.1128/JB.186.12.3911-3921.2004
    • (2004) J Bacteriol , vol.186 , pp. 3911-3921
    • Fukiya, S.1    Mizoguchi, H.2    Tobe, T.3    Mori, H.4
  • 25
  • 27
    • 34250682175 scopus 로고    scopus 로고
    • Subtyping method for Escherichia coli shiga toxin (verocytotoxin) 2 variants and correlations to clinical manifestations
    • 1933035 17446326 10.1128/JCM.02591-06
    • Persson S Olsen KE Ethelberg S Scheutz F Subtyping method for Escherichia coli shiga toxin (verocytotoxin) 2 variants and correlations to clinical manifestations J Clin Microbiol 2007, 45:2020-4 1933035 17446326 10.1128/JCM.02591-06
    • (2007) J Clin Microbiol , vol.45 , pp. 2020-2024
    • Persson, S.1    Olsen, K.E.2    Ethelberg, S.3    Scheutz, F.4
  • 29
    • 0003418494 scopus 로고    scopus 로고
    • Epidemiology, study, design and data analysis
    • Ca Hall
    • Woodward M Epidemiology, study, design and data analysis Texts in Statistical Science Ca Hall 1999
    • (1999) Texts in Statistical Science
    • Woodward, M.1
  • 30
    • 25444483377 scopus 로고    scopus 로고
    • A new approach for the analysis of bacterial microarray-based Comparative Genomic Hybridization: Insights from an empirical study
    • 1168892 15918914 10.1186/1471-2164-6-78
    • Taboada EN Acedillo RR Luebbert CC Findlay WA Nash JH A new approach for the analysis of bacterial microarray-based Comparative Genomic Hybridization: Insights from an empirical study BMC Genomics 2005, 6:78 1168892 15918914 10.1186/1471-2164-6-78
    • (2005) BMC Genomics , vol.6 , pp. 78
    • Taboada, E.N.1    Acedillo, R.R.2    Luebbert, C.C.3    Findlay, W.A.4    Nash, J.H.5
  • 31
    • 40449099650 scopus 로고    scopus 로고
    • Genetic Diversity among Escherichia coli O157:H7 Isolates and identification of genes linked to human infections
    • Wu G Carter B Mafura M Liebana E Woodward MJ Anjum MF Genetic Diversity among Escherichia coli O157:H7 Isolates and identification of genes linked to human infections Infect Immun 2007
    • (2007) Infect Immun
    • Wu, G.1    Carter, B.2    Mafura, M.3    Liebana, E.4    Woodward, M.J.5    Anjum, M.F.6
  • 32
    • 0036640105 scopus 로고    scopus 로고
    • Co-expression pattern from DNA microarray experiments as a tool for operon prediction
    • 117043 12087173 10.1093/nar/gkf388
    • Sabatti C Rohlin L Oh MK Liao JC Co-expression pattern from DNA microarray experiments as a tool for operon prediction Nucleic Acids Res 2002, 30:2886-93 117043 12087173 10.1093/nar/gkf388
    • (2002) Nucleic Acids Res , vol.30 , pp. 2886-2893
    • Sabatti, C.1    Rohlin, L.2    Oh, M.K.3    Liao, J.C.4
  • 33
    • 33748873904 scopus 로고    scopus 로고
    • The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella
    • 10.1186/1471-2164-7-218 16939645
    • Peng J Zhang X Yang J Wang J Yang E Bin W Wei C Sun M Jin Q The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella BMC Genomics 2006, 7:218 10.1186/1471-2164-7-218 16939645
    • (2006) BMC Genomics , vol.7 , pp. 218
    • Peng, J.1    Zhang, X.2    Yang, J.3    Wang, J.4    Yang, E.5    Bin, W.6    Wei, C.7    Sun, M.8    Jin, Q.9
  • 34
    • 34250668784 scopus 로고    scopus 로고
    • Comparative genomics of Canadian epidemic lineages of methicillin-resistant Staphylococcus aureus
    • 1933033 17428941 10.1128/JCM.02500-06
    • Christianson S Golding GR Campbell J Mulvey MR Comparative genomics of Canadian epidemic lineages of methicillin-resistant Staphylococcus aureus J Clin Microbiol 2007, 45:1904-11 1933033 17428941 10.1128/ JCM.02500-06
    • (2007) J Clin Microbiol , vol.45 , pp. 1904-1911
    • Christianson, S.1    Golding, G.R.2    Campbell, J.3    Mulvey, M.R.4
  • 36
    • 4944220181 scopus 로고    scopus 로고
    • Comparative genomics of gene-family size in closely related bacteria
    • 395786 15059260 10.1186/gb-2004-5-4-r27
    • Pushker R Mira A Rodriguez-Valera F Comparative genomics of gene-family size in closely related bacteria Genome Biol 2004, 5:R27 395786 15059260 10.1186/gb-2004-5-4-r27
    • (2004) Genome Biol , vol.5
    • Pushker, R.1    Mira, A.2    Rodriguez-Valera, F.3
  • 38
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • 100354 11842121 10.1093/nar/30.4.e15
    • Yang YH Dudoit S Luu P Lin DM Peng V Ngai J Speed TP Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 2002, 30:e15 100354 11842121 10.1093/nar/30.4.e15
    • (2002) Nucleic Acids Res , vol.30
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 39
    • 0012572299 scopus 로고    scopus 로고
    • A variance-stabilizing transformation for gene-expression microarray data
    • 12169537
    • Durbin BP Hardin JS Hawkins DM Rocke DM A variance-stabilizing transformation for gene-expression microarray data Bioinformatics 2002, 18(Suppl 1):S105-10 12169537
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Durbin, B.P.1    Hardin, J.S.2    Hawkins, D.M.3    Rocke, D.M.4
  • 41
    • 33749010313 scopus 로고    scopus 로고
    • Comparison of different approaches for comparative genetic analysis using microarray hybridization
    • 10.1007/s00253-006-0536-x 16933134
    • Pin C Reuter M Pearson B Friis L Overweg K Baranyi J Wells J Comparison of different approaches for comparative genetic analysis using microarray hybridization Appl Microbiol Biotechnol 2006, 72:852-9 10.1007/s00253-006-0536-x 16933134
    • (2006) Appl Microbiol Biotechnol , vol.72 , pp. 852-859
    • Pin, C.1    Reuter, M.2    Pearson, B.3    Friis, L.4    Overweg, K.5    Baranyi, J.6    Wells, J.7
  • 42
    • 30744464935 scopus 로고    scopus 로고
    • Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics
    • 1287626 16269792 10.1128/AEM.71.11.7504-7514.2005
    • Witney AA Marsden GL Holden MT Stabler RA Husain SE Vass JK Butcher PD Hinds J Lindsay JA Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics Appl Environ Microbiol 2005, 71:7504-14 1287626 16269792 10.1128/ AEM.71.11.7504-7514.2005
    • (2005) Appl Environ Microbiol , vol.71 , pp. 7504-7514
    • Witney, A.A.1    Marsden, G.L.2    Holden, M.T.3    Stabler, R.A.4    Husain, S.E.5    Vass, J.K.6    Butcher, P.D.7    Hinds, J.8    Lindsay, J.A.9
  • 44
  • 47
    • 0035433128 scopus 로고    scopus 로고
    • Quantitative quality control in microarray image processing and data acquisition
    • 55840 11470890 10.1093/nar/29.15.e75
    • Wang X Ghosh S Guo SW Quantitative quality control in microarray image processing and data acquisition Nucleic Acids Res 2001, 29:E75-5 55840 11470890 10.1093/nar/29.15.e75
    • (2001) Nucleic Acids Res , vol.29
    • Wang, X.1    Ghosh, S.2    Guo, S.W.3
  • 48
    • 0142246576 scopus 로고    scopus 로고
    • Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays
    • 10.1016/S0014-5793(03)01164-5 14596944
    • Pearson BM Pin C Wright J I'Anson K Humphrey T Wells JM Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays FEBS Lett 2003, 554:224-30 10.1016/S0014-5793(03)01164-5 14596944
    • (2003) FEBS Lett , vol.554 , pp. 224-230
    • Pearson, B.M.1    Pin, C.2    Wright, J.3    I'Anson, K.4    Humphrey, T.5    Wells, J.M.6
  • 49
    • 0037195198 scopus 로고    scopus 로고
    • Improved analytical methods for microarray-based genome-composition analysis
    • RESEARCH0065 133449 12429064 10.1186/gb-2002-3-11-research0065
    • Kim CC Joyce EA Chan K Falkow S Improved analytical methods for microarray-based genome-composition analysis Genome Biol 2002 3:RESEARCH0065 133449 12429064 10.1186/gb-2002-3-11-research0065
    • (2002) Genome Biol , vol.3
    • Kim, C.C.1    Joyce, E.A.2    Chan, K.3    Falkow, S.4
  • 53
    • 34247326891 scopus 로고    scopus 로고
    • Mixture models as a method to find present and divergent genes in comparative genomic hybridization studies on bacteria
    • 10.1002/bimj.200510286 17476947
    • Feten G Almoy T Snipen L Aakra A Nyquist OL Aastveit AH Mixture models as a method to find present and divergent genes in comparative genomic hybridization studies on bacteria Biom J 2007, 49:242-58 10.1002/ bimj.200510286 17476947
    • (2007) Biom J , vol.49 , pp. 242-258
    • Feten, G.1    Almoy, T.2    Snipen, L.3    Aakra, A.4    Nyquist, O.L.5    Aastveit, A.H.6
  • 54
    • 40449120858 scopus 로고    scopus 로고
    • Statistical methodology for the analysis of microarray data
    • Reading: University of Reading
    • Carter BR Statistical methodology for the analysis of microarray data PhD Thesis Reading: University of Reading 2005
    • (2005) PhD Thesis
    • Carter, B.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.