메뉴 건너뛰기




Volumn 4, Issue 10, 2008, Pages

Fusion and fission of genes define a metric between fungal genomes

Author keywords

[No Author keywords available]

Indexed keywords

FORESTRY; FUNGI; PROTEINS;

EID: 55449129926     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000200     Document Type: Article
Times cited : (23)

References (48)
  • 1
    • 0035500899 scopus 로고    scopus 로고
    • Recent duplication, domain accretion and the dynamic mutation of the human genome
    • Eichler EE (2001) Recent duplication, domain accretion and the dynamic mutation of the human genome. Trends in Genetics 17: 661-669.
    • (2001) Trends in Genetics , vol.17 , pp. 661-669
    • Eichler, E.E.1
  • 2
    • 0035753236 scopus 로고    scopus 로고
    • Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions
    • Enright AJ, Ouzounis CA (2001) Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biology 2: 00341-00347.
    • (2001) Genome Biology , vol.2 , pp. 00341-00347
    • Enright, A.J.1    Ouzounis, C.A.2
  • 3
    • 0034940467 scopus 로고    scopus 로고
    • Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes
    • Yanai I, Derti A, DeLisi C (2001) Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc Natl Acad Sci U S A 98: 7940-7945.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 7940-7945
    • Yanai, I.1    Derti, A.2    DeLisi, C.3
  • 4
    • 33745611416 scopus 로고    scopus 로고
    • Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
    • Pasek S, Risler JL, Brézellec P (2006) Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins. Bioinformatics 22: 1418-1423.
    • (2006) Bioinformatics , vol.22 , pp. 1418-1423
    • Pasek, S.1    Risler, J.L.2    Brézellec, P.3
  • 5
    • 0033621536 scopus 로고    scopus 로고
    • Genome evolution. gene fusion versus gene fission
    • Snel B, Bork P, Huynen M (2000) Genome evolution. gene fusion versus gene fission. Trends in Genetics. pp 9-11.
    • (2000) Trends in Genetics , pp. 9-11
    • Snel, B.1    Bork, P.2    Huynen, M.3
  • 6
    • 27344451557 scopus 로고    scopus 로고
    • Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer
    • Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310: 644-648.
    • (2005) Science , vol.310 , pp. 644-648
    • Tomlins, S.A.1    Rhodes, D.R.2    Perner, S.3    Dhanasekaran, S.M.4    Mehra, R.5
  • 8
    • 2442576123 scopus 로고    scopus 로고
    • Duplicationdegeneration as a mechanism of gene fission and the origin of new genes in Drosophila species
    • Wang W, Yu H, Long M (2004) Duplicationdegeneration as a mechanism of gene fission and the origin of new genes in Drosophila species. Nature Genetics 36: 523-527.
    • (2004) Nature Genetics , vol.36 , pp. 523-527
    • Wang, W.1    Yu, H.2    Long, M.3
  • 10
    • 13144259695 scopus 로고    scopus 로고
    • Relative rates of gene fusion and fission in multi-domain proteins
    • Kummerfeld SK, Teichmann SA (2005) Relative rates of gene fusion and fission in multi-domain proteins. Trends in Genetics 21: 25-30.
    • (2005) Trends in Genetics , vol.21 , pp. 25-30
    • Kummerfeld, S.K.1    Teichmann, S.A.2
  • 11
    • 33646101827 scopus 로고    scopus 로고
    • Genome-wide analysis of mammalian dna segment fusion/fission
    • Zhang Z, Sun H, Zhang Y, Zhao Y, Shi B, et al. (2006) Genome-wide analysis of mammalian dna segment fusion/fission. J Theor Biol 240: 200-208.
    • (2006) J Theor Biol , vol.240 , pp. 200-208
    • Zhang, Z.1    Sun, H.2    Zhang, Y.3    Zhao, Y.4    Shi, B.5
  • 12
    • 0033523989 scopus 로고    scopus 로고
    • Protein interaction maps for complete genomes based on gene fusion events
    • Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90.
    • (1999) Nature , vol.402 , pp. 86-90
    • Enright, A.J.1    Iliopoulos, I.2    Kyrpides, N.C.3    Ouzounis, C.A.4
  • 13
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte EM, Pellegrini M, Ho-Leung N, Rice DW, Yeates TO, et al. (1999) Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753.
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.M.1    Pellegrini, M.2    Ho-Leung, N.3    Rice, D.W.4    Yeates, T.O.5
  • 15
    • 0038724989 scopus 로고    scopus 로고
    • Finding functional features in Saccharomyces genomes by phylogenetic footprinting
    • Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
    • (2003) Science , vol.301 , pp. 71-76
    • Cliften, P.1    Sudarsanam, P.2    Desikan, A.3    Fulton, L.4    Fulton, B.5
  • 16
    • 33644877429 scopus 로고    scopus 로고
    • Genolevures complete genomes provide data and tools for comparative genomics of hemiascomecetous yeasts
    • Sherman D, Durrens P, Iragne F, Beyne E, Nikolski M, et al. (2006) Genolevures complete genomes provide data and tools for comparative genomics of hemiascomecetous yeasts. Nucleic Acids Research 34: D432-D435. http:// cbi.labri.fr/Genolevures/.
    • (2006) Nucleic Acids Research , vol.34
    • Sherman, D.1    Durrens, P.2    Iragne, F.3    Beyne, E.4    Nikolski, M.5
  • 17
    • 0033638015 scopus 로고    scopus 로고
    • CAST: An iterative algorithm for the complexity analysis of sequence tracts
    • Promponas VJ, Enright AJ, Tsoka S, Kreil DP, Leroy C, et al. (2000) CAST: an iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics 16: 915-922.
    • (2000) Bioinformatics , vol.16 , pp. 915-922
    • Promponas, V.J.1    Enright, A.J.2    Tsoka, S.3    Kreil, D.P.4    Leroy, C.5
  • 19
    • 33846680494 scopus 로고    scopus 로고
    • Family relationships: Should consensus reign? - consensus clustering for protein families
    • Nikolski M, Sherman DJ (2007) Family relationships: should consensus reign? - consensus clustering for protein families. Bioinformatics 23: e71-e76.
    • (2007) Bioinformatics , vol.23
    • Nikolski, M.1    Sherman, D.J.2
  • 20
    • 0034623005 scopus 로고    scopus 로고
    • TCoffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame C, Higgins DG, Heringa J (2000) TCoffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 21
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Söding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21: 951-960.
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Söding, J.1
  • 22
    • 55449127001 scopus 로고    scopus 로고
    • Krzywinski M (2005) http://mkweb.bcgsc.ca/circos/.
    • (2005)
    • Krzywinski, M.1
  • 24
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • The Gene Ontology Consortium
    • The Gene Ontology Consortium (2000) Gene ontology: tool for the unification of biology. Nature Genetics 25: 25-29.
    • (2000) Nature Genetics , vol.25 , pp. 25-29
  • 25
    • 33845452848 scopus 로고    scopus 로고
    • A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
    • Fitzpatrick DA, Logue ME, Stajich JE, Butler G (2005) A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evolutionary Biology 6: 99-114.
    • (2005) BMC Evolutionary Biology , vol.6 , pp. 99-114
    • Fitzpatrick, D.A.1    Logue, M.E.2    Stajich, J.E.3    Butler, G.4
  • 26
    • 33745736295 scopus 로고    scopus 로고
    • Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution
    • Dujon B (2006) Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends in Genetics 22: 375-387.
    • (2006) Trends in Genetics , vol.22 , pp. 375-387
    • Dujon, B.1
  • 27
    • 39749134935 scopus 로고    scopus 로고
    • Denoising inferred functional association networks obtained by gene fusion analysis
    • Kamburov A, Goldovsky L, Freilich S, Kapazoglou A, Kunin V, et al. (2007) Denoising inferred functional association networks obtained by gene fusion analysis. BMC Genomics 8: 460.
    • (2007) BMC Genomics , vol.8 , pp. 460
    • Kamburov, A.1    Goldovsky, L.2    Freilich, S.3    Kapazoglou, A.4    Kunin, V.5
  • 28
  • 29
    • 0024339081 scopus 로고
    • Organization of the yeast URA2 gene: Identification of a defective dihydroorotase-like domain in the multifunctional carbamoylphosphate synthetaseaspartate transcarbamylase complex
    • Souciet JL, Nagy M, Gouar ML, Lacroute F, Potier S (1989) Organization of the yeast URA2 gene: identification of a defective dihydroorotase-like domain in the multifunctional carbamoylphosphate synthetaseaspartate transcarbamylase complex. Gene 79: 59-70.
    • (1989) Gene , vol.79 , pp. 59-70
    • Souciet, J.L.1    Nagy, M.2    Gouar, M.L.3    Lacroute, F.4    Potier, S.5
  • 30
    • 0033780375 scopus 로고    scopus 로고
    • Prediction of protein interactions: Metabolic enzymes are frequently involved in gene fusion
    • Tsoka S, Ouzounis C (2000) Prediction of protein interactions: metabolic enzymes are frequently involved in gene fusion. Nature Genetics 26: 141-142.
    • (2000) Nature Genetics , vol.26 , pp. 141-142
    • Tsoka, S.1    Ouzounis, C.2
  • 31
    • 0034625235 scopus 로고    scopus 로고
    • The impact of comparative genomics on our understanding of evolution
    • Koonin EV, Aravind L, Kondrashov A (2000) The impact of comparative genomics on our understanding of evolution. Cell 101: 573-576.
    • (2000) Cell , vol.101 , pp. 573-576
    • Koonin, E.V.1    Aravind, L.2    Kondrashov, A.3
  • 32
    • 12344261833 scopus 로고    scopus 로고
    • The relationship between duplication and recombination
    • Vogel C, Teichmann SA, Pereira-Leal J (2004) The relationship between duplication and recombination. J Mol Biol 346: 355-365.
    • (2004) J Mol Biol , vol.346 , pp. 355-365
    • Vogel, C.1    Teichmann, S.A.2    Pereira-Leal, J.3
  • 33
    • 0036301445 scopus 로고    scopus 로고
    • Proteins with class α/β fold have high-level participation in fusion events
    • Hua S, Guo T, Gough J, Sun Z (2002) Proteins with class α/β fold have high-level participation in fusion events. J Mol Biol 320: 713-719.
    • (2002) J Mol Biol , vol.320 , pp. 713-719
    • Hua, S.1    Guo, T.2    Gough, J.3    Sun, Z.4
  • 34
    • 12744263078 scopus 로고    scopus 로고
    • Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    • Bourque G, Zdobnov EM, Bork P, Pevzner PA, Tesler G (2003) Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res 15: 98-110.
    • (2003) Genome Res , vol.15 , pp. 98-110
    • Bourque, G.1    Zdobnov, E.M.2    Bork, P.3    Pevzner, P.A.4    Tesler, G.5
  • 36
    • 0037609538 scopus 로고    scopus 로고
    • Cloning of an Alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation
    • Davis IJ, Hsi BL, Arroyo JD, Vargas SO, Yeh YA, et al. (2003) Cloning of an Alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation. Proc Natl Acad Sci U S A. pp 6051-6056.
    • (2003) Proc Natl Acad Sci U S A , pp. 6051-6056
    • Davis, I.J.1    Hsi, B.L.2    Arroyo, J.D.3    Vargas, S.O.4    Yeh, Y.A.5
  • 37
    • 0035895567 scopus 로고    scopus 로고
    • Birth of two chimeric genes in the hominidae lineage
    • Courseaux A, Nahon JL (2001) Birth of two chimeric genes in the hominidae lineage. Science 291: 1293-1297.
    • (2001) Science , vol.291 , pp. 1293-1297
    • Courseaux, A.1    Nahon, J.L.2
  • 38
    • 20444468864 scopus 로고    scopus 로고
    • Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae
    • Hall C, Brachat S, Dietrich FS (2005) Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell 4: 1102-1115.
    • (2005) Eukaryot Cell , vol.4 , pp. 1102-1115
    • Hall, C.1    Brachat, S.2    Dietrich, F.S.3
  • 39
    • 3543049575 scopus 로고    scopus 로고
    • Recovery of a function involving gene duplication by retroposition in Saccharomyces cerevisiae
    • Schacherer J, Tourette Y, Souciet JL, Potier S, de Montigny J (2004) Recovery of a function involving gene duplication by retroposition in Saccharomyces cerevisiae. Genome Res 14: 1291-1297.
    • (2004) Genome Res , vol.14 , pp. 1291-1297
    • Schacherer, J.1    Tourette, Y.2    Souciet, J.L.3    Potier, S.4    de Montigny, J.5
  • 40
    • 0027441281 scopus 로고
    • Trans-splicing of pre-mRNA in plants, animals, and protists
    • Bonen L (1993) Trans-splicing of pre-mRNA in plants, animals, and protists. FASEB J 7: 40-46.
    • (1993) FASEB J , vol.7 , pp. 40-46
    • Bonen, L.1
  • 43
    • 13444273437 scopus 로고    scopus 로고
    • The Ashbya genome database (AGD)-a tool for the yeast community and genome biologists
    • Hermida L, Brachat S, Voegeli S, Philippsen P, Primig M (2005) The Ashbya genome database (AGD)-a tool for the yeast community and genome biologists. Nucleic Acids Research 33: D348-D352. http://agd.unibas.ch/.
    • (2005) Nucleic Acids Research , vol.33
    • Hermida, L.1    Brachat, S.2    Voegeli, S.3    Philippsen, P.4    Primig, M.5
  • 44
    • 13444283822 scopus 로고    scopus 로고
    • d'Enfert C, Goyard S, Rodriguez-Arnaveilhe S, Frangeul L, Jones L, et al. (2005) Candidadb: a genome database for Candida albicans pathogenomics. Nucleic Acids Research 33: D353-D357. [Sequence data for Candida albicans was obtained from the Stanford Genome Technology Center website at http://www-sequence.stanford.edu/group/candida. Sequencing of Candida albicans was accomplished with the support of the NIDR and the Burroughs Wellcome Fund.].
    • d'Enfert C, Goyard S, Rodriguez-Arnaveilhe S, Frangeul L, Jones L, et al. (2005) Candidadb: a genome database for Candida albicans pathogenomics. Nucleic Acids Research 33: D353-D357. [Sequence data for Candida albicans was obtained from the Stanford Genome Technology Center website at http://www-sequence.stanford.edu/group/candida. Sequencing of Candida albicans was accomplished with the support of the NIDR and the Burroughs Wellcome Fund.].
  • 45
    • 0037464589 scopus 로고    scopus 로고
    • The genome sequence of the filamentous fungus Neurospora crassa
    • Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read N, et al. (2003) The genome sequence of the filamentous fungus Neurospora crassa. Nature 422: 859-868.
    • (2003) Nature , vol.422 , pp. 859-868
    • Galagan, J.E.1    Calvo, S.E.2    Borkovich, K.A.3    Selker, E.U.4    Read, N.5
  • 46
    • 28844461287 scopus 로고    scopus 로고
    • Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae
    • Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, et al. (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1105-1115.
    • (2005) Nature , vol.438 , pp. 1105-1115
    • Galagan, J.E.1    Calvo, S.E.2    Cuomo, C.3    Ma, L.J.4    Wortman, J.R.5
  • 47
    • 0037148758 scopus 로고    scopus 로고
    • The genome sequence of Schizosaccharomyces pombe
    • Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, et al. (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415: 845-848. http://www.sanger.ac.uk/Projects/S_pombe/.
    • (2002) Nature , vol.415 , pp. 845-848
    • Wood, V.1    Gwilliam, R.2    Rajandream, M.A.3    Lyne, M.4    Lyne, R.5
  • 48
    • 20044380139 scopus 로고    scopus 로고
    • The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans
    • Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, et al. (2005) The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science 307: 1321-1324.
    • (2005) Science , vol.307 , pp. 1321-1324
    • Loftus, B.J.1    Fung, E.2    Roncaglia, P.3    Rowley, D.4    Amedeo, P.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.