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

Journal of Computational Biology

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

  Hoberman, Rose ^a   Sankoff, David ^b   Durand, Dannie ^c  

^a Carnegie Mellon University   (United States)

^b UNIVERSITY OF OTTAWA   (Canada)

^c CARNEGIE MELLON UNIVERSITY   (United States)

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;

BACILLUS SUBTILIS; CHROMOSOME MAPPING; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENES; GENOME; GENOMICS; MODELS, GENETIC; MULTIGENE FAMILY; PROBABILITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 27644546689     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2005.12.1083     Document Type: Article

References (48)

1. Abi-Rached, L., Gilles, A., Shiina, T., Pontarotti, P., and Inoko, H. 2002. Evidence of en bloc duplication in vertebrate genomes. Nat. Genet. 31, 100-105.
2. Amores, A., Force, A., Yan, Y., Joly, L., Amemiya, C., Fritz, A., Ho, R., Langeland, J., Prince, V., Wang, Y.L., Westerfield, M., Ekker, M., and Postlethwait, J.H. 1998. Zebrafish box clusters and vertebrate genome evolution. Science 282, 1711-1714.
3. Bansal, A.K. 1999. An automated comparative analysis of 17 complete microbial genomes. Bioinformatics 15, 900-908. www.cs.kent.edu/~arvind/orthos. html.
4. Bergeron, A., Corteel, S., and Raffinot, M. 2002. The algorithmic of gene teams. WABI, Lecture Notes in Computer Science 2452, 464-476. www-igm.univ-mlv.fr/~raffinot/geneteam.html.
5. 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.
6. Blanchette, M., Kunisawa, T., and Sankoff, D. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49, 193-203.
7. 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.
8. 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.
9. 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.
10. 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.
11. 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.
12. 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.
13. Danchin, E.G.J., Abi-Rached, L., Gilles, A., and Pontarotti, P. 2003. Conservation of the MHC-like region throughout evolution. Immunogenetics 55, 141-148.
14. Durand, D., and Sankoff, D. 2003. Tests for gene clustering. J. Comp. Biol. 453-482.
15. Endo, T., Imanishi, T., Gojobori, T., and Inoko, H. 1997. Evolutionary significance of intra-genome duplications on human chromosomes. Gene 205, 19-27.
16. Friedman, R., and Hughes, A.L. 2001. Gene duplication and the structure of eukaryotic genomes. Genome Res. 11, 373-381.
17. Gibson, T., and Spring, J. 2000. Evidence in favour of ancient octaploidy in the vertebrate genome. Biochem. Soc. Trans. 2, 259-264.
18. Graham, R.L., Knuth, D.E., and Patashnik, O. 1989. Concrete Mathematics, Addison-Wesley, Reading, MA.
19. Hampson, S.E., Gaut, B.S., and Baldi, P. 2005. Statistical detection of chromosomal homology using shared-gene density alone. Bioinformatics 21, 1339-1348.
20. 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.
21. Hoberman, R., Sankoff, D., and Durand, D. 2005. The statistical significance of max-gap clusters. Proc. RECOMB Satellite Workshop on Comparative Genomics, Lecture Notes in Bioinformatics, Springer Verlag. Editor: J. Lagergran, vol. 3388, pgs. 55-71.
22. Hokamp, K. 2001. A Bioinformatics Approach to (Intra-)Genome Comparisons. Ph.D Thesis, University of Dublin, Trinity College.
23. 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.
24. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
25. 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.
26. 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.
27. Lawrence, J., and Roth, J.R. 1996. Selfish operons: Horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843-1860.
28. 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.
29. 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.
30. McLysaght, A., Hokamp, K., and Wolfe, K.H. 2002. Extensive genomic duplication during early chordate evolution. Nature Genet. 31, 200-204.
31. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D., and Maltsev, N. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96, 2896-2901.
32. 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.
33. 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.
34. Salgado, H., Gama-Castro, S., Martínez-Antonio, A., Díaz-Peredo, E., Sánchez-Solano, F., Peralta-Gil, M., Garcia-Alonso, D., Jiménez-Jacinto, V., Santos-Zavaleta, A., Bonavides-Martínez, C., and Collado-Vides, J. 2004. RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucl. Acids Res. 32, D303-D306.
35. Sankoff, D. 2003. Rearrangements and chromosomal evolution. Curr. Opin. Genet. Dev. 13, 583-587.
36. 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.
37. 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.
38. 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.
39. Simillion, C., Vandepoele, K., Montagu, M.V., Zabeau, M., and de Peer, Y.V. 2002. The hidden duplication past of Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 99, 13627-13632.
40. 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.
41. Tamames, J. 2001. Evolution of gene order conservation in prokaryotes. Genome Biol. 6, 0020.1-0020.11.
42. Tamames, J., Gonzalez-Moreno, M., Valencia, A., and Vicente, M. 2001. Bringing gene order into bacterial shape. Trends Genet. 3, 124-126.
43. Trachtulec, Z., and Forejt, J. 2001. Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast. Mamm. Genome 3, 227-231.
44. Uspensky, J.V. 1937. Introduction to Mathematical Probability, 23-24, McGraw-Hill, New York.
45. 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.
46. Vision, T.J., Brown, D.G., and Tanksley, S.D. 2000. The origins of genomic duplications in Arabidopsis. Science 290, 2114-2117.
47. Wolfe, K. 2001. Yesterday's polyploids and the mystery of diploidization. Nature Rev. Genet. 2, 33-41.
48. Zheng, Y, Szustakowski, J.D., Fortnow, L., Roberts, R.J., and Kasif, S. 2002. Computational identification of operons in microbial genomes. Genome Res. 12, 1221-1230.