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Volumn 12, Issue 8, 2005, Pages 1083-1102

The statistical analysis of spatially clustered genes under the maximum gap criterion

Author keywords

Comparative genomics; Gene teams; Genome evolution; Genome rearrangements; Max gap clusters

Indexed keywords

ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENETICS; BACTERIAL GENOME; ESCHERICHIA COLI; GENE CLUSTER; GENOMICS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; STATISTICAL ANALYSIS;

EID: 27644546689     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2005.12.1083     Document Type: Article
Times cited : (28)

References (48)
  • 3
    • 0033384634 scopus 로고    scopus 로고
    • An automated comparative analysis of 17 complete microbial genomes
    • Bansal, A.K. 1999. An automated comparative analysis of 17 complete microbial genomes. Bioinformatics 15, 900-908. www.cs.kent.edu/~arvind/orthos. html.
    • (1999) Bioinformatics , vol.15 , pp. 900-908
    • Bansal, A.K.1
  • 5
    • 0037313579 scopus 로고    scopus 로고
    • A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome
    • Blanc, G., Hokamp, K., and Wolfe, K.H. 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13, 137-144.
    • (2003) Genome Res. , vol.13 , pp. 137-144
    • Blanc, G.1    Hokamp, K.2    Wolfe, K.H.3
  • 6
    • 0032770572 scopus 로고    scopus 로고
    • Gene order breakpoint evidence in animal mitochondrial phylogeny
    • Blanchette, M., Kunisawa, T., and Sankoff, D. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49, 193-203.
    • (1999) J. Mol. Evol. , vol.49 , pp. 193-203
    • Blanchette, M.1    Kunisawa, T.2    Sankoff, D.3
  • 7
    • 12744263078 scopus 로고    scopus 로고
    • Comparativie architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    • Bourque, G., Zdobnov, E., Bork, P., Pevzner, P., and Telser, G. 2005. Comparativie architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15, 98-110.
    • (2005) Genome Res. , vol.15 , pp. 98-110
    • Bourque, G.1    Zdobnov, E.2    Bork, P.3    Pevzner, P.4    Telser, G.5
  • 8
    • 1042276327 scopus 로고    scopus 로고
    • Fast identification and statistical evaluation of segmental homologies in comparative maps
    • Calabrese, P.P., Chakravarty, S., and Vision, T.J. 2003. Fast identification and statistical evaluation of segmental homologies in comparative maps. ISMB (Supplement of Bioinformatics) 74-80.
    • (2003) ISMB (Supplement of Bioinformatics) , pp. 74-80
    • Calabrese, P.P.1    Chakravarty, S.2    Vision, T.J.3
  • 9
    • 2942610254 scopus 로고    scopus 로고
    • DiagHunter and GenoPix2D: Programs for genomic comparisons, large-scale homology discovery and visualization
    • Cannon, S.B., Kozik, A., Chan, B., Michelmore, R., and Young, N.D. 2003. DiagHunter and GenoPix2D: Programs for genomic comparisons, large-scale homology discovery and visualization. Genome Biol. 4, R68.
    • (2003) Genome Biol. , vol.4
    • Cannon, S.B.1    Kozik, A.2    Chan, B.3    Michelmore, R.4    Young, N.D.5
  • 10
    • 2342512807 scopus 로고    scopus 로고
    • Operon prediction by comparative genomics: An application to the Synechococcus sp. WH8102 genome
    • Chen, X., Su, Z., Dam, P., Palenik, B., Xu, Y., and Jiang, T. 2004. Operon prediction by comparative genomics: An application to the Synechococcus sp. WH8102 genome. Nucl. Acids Res. 32, 2147-2157.
    • (2004) Nucl. Acids Res. , vol.32 , pp. 2147-2157
    • Chen, X.1    Su, Z.2    Dam, P.3    Palenik, B.4    Xu, Y.5    Jiang, T.6
  • 11
    • 0001800180 scopus 로고    scopus 로고
    • An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae
    • Sankoff, D., and Nadeau, J.H., eds., Kluwer Academic Press, Dordrecht, NL
    • Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.-S., Warnow, T., and Wyman, S. 2000. An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae, in Sankoff, D., and Nadeau, J.H., eds., Comparative Genomics, 99-121, Kluwer Academic Press, Dordrecht, NL.
    • (2000) Comparative Genomics , pp. 99-121
    • Cosner, M.E.1    Jansen, R.K.2    Moret, B.M.E.3    Raubeson, L.A.4    Wang, L.-S.5    Warnow, T.6    Wyman, S.7
  • 12
    • 0031024921 scopus 로고    scopus 로고
    • Of worms and men: An evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families
    • Coulier, F., Pontarotti, P., Roubin, R., Hartung, H., Goldfarb, M., and Birnbaum, D., 1997. Of worms and men: An evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families. J. Mol. Evol. 44, 43-56.
    • (1997) J. Mol. Evol. , vol.44 , pp. 43-56
    • Coulier, F.1    Pontarotti, P.2    Roubin, R.3    Hartung, H.4    Goldfarb, M.5    Birnbaum, D.6
  • 14
    • 0242606435 scopus 로고    scopus 로고
    • Tests for gene clustering
    • Durand, D., and Sankoff, D. 2003. Tests for gene clustering. J. Comp. Biol. 453-482.
    • (2003) J. Comp. Biol. , pp. 453-482
    • Durand, D.1    Sankoff, D.2
  • 15
    • 0031593209 scopus 로고    scopus 로고
    • Evolutionary significance of intra-genome duplications on human chromosomes
    • Endo, T., Imanishi, T., Gojobori, T., and Inoko, H. 1997. Evolutionary significance of intra-genome duplications on human chromosomes. Gene 205, 19-27.
    • (1997) Gene , vol.205 , pp. 19-27
    • Endo, T.1    Imanishi, T.2    Gojobori, T.3    Inoko, H.4
  • 16
    • 0035081235 scopus 로고    scopus 로고
    • Gene duplication and the structure of eukaryotic genomes
    • Friedman, R., and Hughes, A.L. 2001. Gene duplication and the structure of eukaryotic genomes. Genome Res. 11, 373-381.
    • (2001) Genome Res. , vol.11 , pp. 373-381
    • Friedman, R.1    Hughes, A.L.2
  • 17
    • 0033957089 scopus 로고    scopus 로고
    • Evidence in favour of ancient octaploidy in the vertebrate genome
    • Gibson, T., and Spring, J. 2000. Evidence in favour of ancient octaploidy in the vertebrate genome. Biochem. Soc. Trans. 2, 259-264.
    • (2000) Biochem. Soc. Trans. , vol.2 , pp. 259-264
    • Gibson, T.1    Spring, J.2
  • 19
    • 17444395994 scopus 로고    scopus 로고
    • Statistical detection of chromosomal homology using shared-gene density alone
    • Hampson, S.E., Gaut, B.S., and Baldi, P. 2005. Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics 21, 1339-1348.
    • (2005) Bioinformatics , vol.21 , pp. 1339-1348
    • Hampson, S.E.1    Gaut, B.S.2    Baldi, P.3
  • 20
    • 0028806782 scopus 로고
    • Genome sequence comparison and scenarios for gene rearrangements: A test case
    • Hannenhalli, S., Chappey, C., Koonin, E.V., and Pevzner, P.A. 1995. Genome sequence comparison and scenarios for gene rearrangements: A test case. Genomics 30, 299-311.
    • (1995) Genomics , vol.30 , pp. 299-311
    • Hannenhalli, S.1    Chappey, C.2    Koonin, E.V.3    Pevzner, P.A.4
  • 23
    • 0031830374 scopus 로고    scopus 로고
    • Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1
    • Hughes, A.L. 1998. Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1. Mol. Biol. Evol. 15, 854-870.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 854-870
    • Hughes, A.L.1
  • 24
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 25
    • 0030732316 scopus 로고    scopus 로고
    • New insights into the genomic organization and origin of the major histocompatibility complex: Role of chromosomal (genome) duplication in the emergence of the adaptive immune system
    • Kasahara, M. 1997. New insights into the genomic organization and origin of the major histocompatibility complex: Role of chromosomal (genome) duplication in the emergence of the adaptive immune system. Hereditas 127, 59-65.
    • (1997) Hereditas , vol.127 , pp. 59-65
    • Kasahara, M.1
  • 26
    • 0030200739 scopus 로고    scopus 로고
    • Paralogy mapping: Identification of a region in the human MHC triplicated onto human chromosomes 1 and 9 allows the prediction and isolation of novel PBX and NOTCH loci
    • Katsanis, N., Fitzgibbon, J., and Fisher, E. 1996. Paralogy mapping: Identification of a region in the human MHC triplicated onto human chromosomes 1 and 9 allows the prediction and isolation of novel PBX and NOTCH loci. Genomics 35, 101-108.
    • (1996) Genomics , vol.35 , pp. 101-108
    • Katsanis, N.1    Fitzgibbon, J.2    Fisher, E.3
  • 27
    • 0029847554 scopus 로고    scopus 로고
    • Selfish operons: Horizontal transfer may drive the evolution of gene clusters
    • Lawrence, J., and Roth, J.R. 1996. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843-1860.
    • (1996) Genetics , vol.143 , pp. 1843-1860
    • Lawrence, J.1    Roth, J.R.2
  • 28
    • 0035234701 scopus 로고    scopus 로고
    • A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31
    • Lipovich, L., Lynch, E.D., Lee, M.K., and King, M.-C. 2001. A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31. Genome Biol. 2, 0011.1-0011.13.
    • (2001) Genome Biol. , vol.2
    • Lipovich, L.1    Lynch, E.D.2    Lee, M.K.3    King, M.-C.4
  • 29
    • 0042423438 scopus 로고    scopus 로고
    • Gene teams: A new formalization of gene clusters for comparative genomics
    • Luc, N., Risler, J., Bergeron, A., and Raffinot, M. 2003. Gene teams: A new formalization of gene clusters for comparative genomics. Comp. Biol. Chem. 27, 59-67.
    • (2003) Comp. Biol. Chem. , vol.27 , pp. 59-67
    • Luc, N.1    Risler, J.2    Bergeron, A.3    Raffinot, M.4
  • 30
    • 0036613237 scopus 로고    scopus 로고
    • Extensive genomic duplication during early chordate evolution
    • McLysaght, A., Hokamp, K., and Wolfe, K.H. 2002. Extensive genomic duplication during early chordate evolution. Nature Genet. 31, 200-204.
    • (2002) Nature Genet. , vol.31 , pp. 200-204
    • McLysaght, A.1    Hokamp, K.2    Wolfe, K.H.3
  • 32
    • 0031828161 scopus 로고    scopus 로고
    • Ancient large-scale genome duplications: Phylogenetic and linkage analyses shed light on chordate genome evolution
    • Pebusque, M.-J., Coulier, F., Birnbaum, D., and Pontarotti, P. 1998. Ancient large-scale genome duplications: Phylogenetic and linkage analyses shed light on chordate genome evolution. Mol. Biol. Evol. 15, 1145-1159.
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1145-1159
    • Pebusque, M.-J.1    Coulier, F.2    Birnbaum, D.3    Pontarotti, P.4
  • 33
    • 0031104878 scopus 로고    scopus 로고
    • Newly indentified paralogous groups on mouse chromosomes 5 and 11 reveal the age of a T-box cluster duplication
    • Ruvinsky, I., and Silver, L.M. 1997. Newly indentified paralogous groups on mouse chromosomes 5 and 11 reveal the age of a T-box cluster duplication. Genomics 40, 262-266.
    • (1997) Genomics , vol.40 , pp. 262-266
    • Ruvinsky, I.1    Silver, L.M.2
  • 35
    • 0345447448 scopus 로고    scopus 로고
    • Rearrangements and chromosomal evolution
    • Sankoff, D. 2003. Rearrangements and chromosomal evolution. Curr. Opin. Genet. Dev. 13, 583-587.
    • (2003) Curr. Opin. Genet. Dev. , vol.13 , pp. 583-587
    • Sankoff, D.1
  • 36
    • 0033677382 scopus 로고    scopus 로고
    • Early eukaryote evolution based on mitochondrial gene order breakpoints
    • Sankoff, D., Bryant, D., Deneault, M., Lang, B.F., and Burger, G. 2000a. Early eukaryote evolution based on mitochondrial gene order breakpoints. J. Comp. Biol. 3-4, 521-535.
    • (2000) J. Comp. Biol. , vol.3-4 , pp. 521-535
    • Sankoff, D.1    Bryant, D.2    Deneault, M.3    Lang, B.F.4    Burger, G.5
  • 37
    • 0002136285 scopus 로고    scopus 로고
    • Chloroplast gene order and the divergence of plants and algae from the normalized number of induced breakpoints
    • Sankoff, D., and Nadeau, J.H., eds., Kluwer Academic Press, Dordrecht, NL
    • Sankoff, D., Deneault, M., Bryant, D., Lemieux, C., and Turmel, M. 2000b. Chloroplast gene order and the divergence of plants and algae from the normalized number of induced breakpoints, in Sankoff, D., and Nadeau, J.H., eds., Comparative Genomics, 89-98, Kluwer Academic Press, Dordrecht, NL.
    • (2000) Comparative Genomics , pp. 89-98
    • Sankoff, D.1    Deneault, M.2    Bryant, D.3    Lemieux, C.4    Turmel, M.5
  • 38
    • 0141817723 scopus 로고    scopus 로고
    • Chromosome rearrangements in evolution: From gene order to genome sequence and back
    • Sankoff, D., and Nadeau, J.H. 2003. Chromosome rearrangements in evolution: From gene order to genome sequence and back. Proc. Natl. Acad. Sci. USA 100, 11188-11189.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 11188-11189
    • Sankoff, D.1    Nadeau, J.H.2
  • 40
    • 0035424711 scopus 로고    scopus 로고
    • On the total number of genes and their length distribution in complete microbial genomes
    • Skovgaard, M., Jensen, L.J., Brunak, S., Ussery, D., and Krogh, A. 2001. On the total number of genes and their length distribution in complete microbial genomes. Trends Genet. 17, 425-428.
    • (2001) Trends Genet. , vol.17 , pp. 425-428
    • Skovgaard, M.1    Jensen, L.J.2    Brunak, S.3    Ussery, D.4    Krogh, A.5
  • 41
    • 0010414313 scopus 로고    scopus 로고
    • Evolution of gene order conservation in prokaryotes
    • Tamames, J. 2001. Evolution of gene order conservation in prokaryotes. Genome Biol. 6, 0020.1-0020.11.
    • (2001) Genome Biol. , vol.6
    • Tamames, J.1
  • 43
    • 0035099929 scopus 로고    scopus 로고
    • Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast
    • Trachtulec, Z., and Forejt, J. 2001. Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast. Mamm. Genome 3, 227-231.
    • (2001) Mamm. Genome , vol.3 , pp. 227-231
    • Trachtulec, Z.1    Forejt, J.2
  • 45
    • 0036852286 scopus 로고    scopus 로고
    • The automatic detection of homologous re-gions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice
    • Vandepoele, K., Saeys, Y., Simillion, C., Raes, J., and van de Peer, Y. 2002. The automatic detection of homologous re-gions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. 12, 1792-1801.
    • (2002) Genome Res. , vol.12 , pp. 1792-1801
    • Vandepoele, K.1    Saeys, Y.2    Simillion, C.3    Raes, J.4    Van De Peer, Y.5
  • 46
    • 0034671866 scopus 로고    scopus 로고
    • The origins of genomic duplications in Arabidopsis
    • Vision, T.J., Brown, D.G., and Tanksley, S.D. 2000. The origins of genomic duplications in Arabidopsis. Science 290, 2114-2117.
    • (2000) Science , vol.290 , pp. 2114-2117
    • Vision, T.J.1    Brown, D.G.2    Tanksley, S.D.3
  • 47
    • 0035344021 scopus 로고    scopus 로고
    • Yesterday's polyploids and the mystery of diploidization
    • Wolfe, K. 2001. Yesterday's polyploids and the mystery of diploidization. Nature Rev. Genet. 2, 33-41.
    • (2001) Nature Rev. Genet. , vol.2 , pp. 33-41
    • Wolfe, K.1


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