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Volumn 2, Issue 4, 2011, Pages 912-924

Evolution and quantitative comparison of genome-wide protein domain distributions

Author keywords

Eukarya; Functional genome annotation; GO classification; HMM models; Protein domains

Indexed keywords

ZINC FINGER PROTEIN;

EID: 84055193648     PISSN: None     EISSN: 20734425     Source Type: Journal    
DOI: 10.3390/genes2040912     Document Type: Article
Times cited : (5)

References (32)
  • 2
    • 0034625235 scopus 로고    scopus 로고
    • The impact of comparative genomics on ourunderstanding of evolution
    • Koonin, E.; Aravind, L.; Kondrashov, A. The impact of comparative genomics on ourunderstanding of evolution. Cell 2000, 101, 573-576.
    • (2000) Cell , vol.101 , pp. 573-576
    • Koonin, E.1    Aravind, L.2    Kondrashov, A.3
  • 4
    • 0038486929 scopus 로고    scopus 로고
    • An evolutionarily structured universe of proteinarchitecture
    • Caetano-Anolles, G.; Caetano-Anolles, D. An evolutionarily structured universe of proteinarchitecture. Genome Res. 2003, 13, 1563-1571.
    • (2003) Genome Res , vol.13 , pp. 1563-1571
    • Caetano-Anolles, G.1    Caetano-Anolles, D.2
  • 6
    • 77949513721 scopus 로고    scopus 로고
    • The evolutionary history of protein domains viewed by species phylogeny
    • Yang, S.; Bourne, P.E. The evolutionary history of protein domains viewed by species phylogeny. PLoS One 2009, 4, e8378:1-e8378:12.
    • (2009) PLoS On , vol.4
    • Yang, S.1    Bourne, P.E.2
  • 7
    • 77953621315 scopus 로고    scopus 로고
    • Innovation in gene regulation: The case of chromatincomputation
    • Prohaska, S.J.; Stadler, P.F.; Krakauer, D.C. Innovation in gene regulation: The case of chromatincomputation. J. Theor. Biol. 2010, 265, 27-44.
    • (2010) J. Theor. Biol , vol.265 , pp. 27-44
    • Prohaska, S.J.1    Stadler, P.F.2    Krakauer, D.C.3
  • 8
    • 1242352406 scopus 로고    scopus 로고
    • Assessing the impact of alternativesplicing on domain interactions in the human proteome
    • Resch, A.; Xing, Y.; Modrek, B.; Gorlick, M.; Riley, R.; Lee, C. Assessing the impact of alternativesplicing on domain interactions in the human proteome. J. Proteome Res. 2004, 3, 76-83.
    • (2004) J. Proteome Res , vol.3 , pp. 76-83
    • Resch, A.1    Xing, Y.2    Modrek, B.3    Gorlick, M.4    Riley, R.5    Lee, C.6
  • 10
    • 40449095056 scopus 로고    scopus 로고
    • Evolution of protein domain promiscuity ineukaryotes
    • Basu, M.K.; Carmel, L.; Rogozin, I.B.; Koonin, E.V. Evolution of protein domain promiscuity ineukaryotes. Genome Res. 2008, 18, 449-461.
    • (2008) Genome Res , vol.18 , pp. 449-461
    • Basu, M.K.1    Carmel, L.2    Rogozin, I.B.3    Koonin, E.V.4
  • 11
    • 39549096663 scopus 로고    scopus 로고
    • Evolutionary history and functionalimplications of protein domains and their combinations in eukaryotes
    • Itoh, M.; Nacher, J.C.; Kuma, K.I.; Goto, S.; Kanehisa, M. Evolutionary history and functionalimplications of protein domains and their combinations in eukaryotes. Genome Biol. 2007, 8, R121:1-R121:15.
    • (2007) Genome Biol , vol.8
    • Itoh, M.1    Nacher, J.C.2    Kuma, K.I.3    Goto, S.4    Kanehisa, M.5
  • 12
    • 17444407091 scopus 로고    scopus 로고
    • Evolutionary cores of domain co-occurence networks
    • Wuchty, S.; Almaas, E. Evolutionary cores of domain co-occurence networks. BMC Evol. Biol. 2005, 5, 24:1-24:12.
    • (2005) BMC Evol. Biol , vol.5
    • Wuchty, S.1    Almaas, E.2
  • 16
    • 84855831412 scopus 로고    scopus 로고
    • Quantitative Comparison of Genomic-Wide ProteinDomain Distributions
    • Schomburg, D., Grote, A.,Eds.; Gesellschaft f̈ur Informatik: Bonn, Germany
    • Parikesit, A.A.; Stadler, P.F.; Prohaska, S.J. Quantitative Comparison of Genomic-Wide ProteinDomain Distributions. In German Conference on Bioinformatics 2010; Schomburg, D., Grote, A.,Eds.; Gesellschaft f̈ur Informatik: Bonn, Germany, 2010; Volume P-173, pp. 93-102.
    • (2010) German Conference On Bioinformatics 2010 , vol.P-173 , pp. 93-102
    • Parikesit, A.A.1    Stadler, P.F.2    Prohaska, S.J.3
  • 18
    • 78651412161 scopus 로고    scopus 로고
    • Strong functional patterns in the evolution of eukaryotic genomesrevealed by the reconstruction of ancestral protein domain repertoires
    • Zmasek, C.M.; Godzik, A. Strong functional patterns in the evolution of eukaryotic genomesrevealed by the reconstruction of ancestral protein domain repertoires. Genome Biol. 2011, 12, R4:1-R4:13.
    • (2011) Genome Biol , vol.12
    • Zmasek, C.M.1    Godzik, A.2
  • 20
    • 78049250483 scopus 로고    scopus 로고
    • More than 1,001 problems with protein domaindatabases: Transmembrane regions, signal peptides and the issue of sequence homology
    • Wong, W.C.; Maurer-Stroh, S.; Eisenhaber, F. More than 1,001 problems with protein domaindatabases: Transmembrane regions, signal peptides and the issue of sequence homology. PLoSComput. Biol. 2010, 6, e1000867:1-e1000867:19.
    • (2010) PLoSComput. Biol , vol.6
    • Wong, W.C.1    Maurer-Stroh, S.2    Eisenhaber, F.3
  • 21
    • 56849114016 scopus 로고    scopus 로고
    • An overview of the phylogeny and diversity of eukaryotes
    • Baldauf, S.L. An overview of the phylogeny and diversity of eukaryotes. J. Syst. Evol. 2008, 46,263-273.
    • (2008) J. Syst. Evol , vol.46 , pp. 263-273
    • Baldauf, S.L.1
  • 22
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • Burge, C.; Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 1997, 268, 78-94.
    • (1997) J. Mol. Biol , vol.268 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 24
    • 4444339460 scopus 로고    scopus 로고
    • Comparative genomics of transcriptional control in thehuman malaria parasite Plasmodium falciparum
    • Coulson, R.M.R.; Hall, N.; Ouzounis, C. Comparative genomics of transcriptional control in thehuman malaria parasite Plasmodium falciparum. Genome Res. 2004, 14, 1548-1554.
    • (2004) Genome Res , vol.14 , pp. 1548-1554
    • Coulson, R.M.R.1    Hall, N.2    Ouzounis, C.3
  • 25
    • 38049173375 scopus 로고    scopus 로고
    • Cdna sequencesreveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome
    • Lu, F.; Jiang, H.; Ding, J.; Mu, J.; Valenzuela, J.G.; Ribeiro, J.M.C.; Su, X.Z. cDNA sequencesreveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics 2007, 8, 255:1-255:11.
    • (2007) BMC Genomics , vol.8
    • Lu, F.1    Jiang, H.2    Ding, J.3    Mu, J.4    Valenzuela, J.G.5    Ribeiro, J.M.C.6    Su, X.Z.7
  • 28
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S.R. Profile hidden Markov models. Bioinformatics 1998, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 30
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: Interactive sequence similaritysearching
    • Finn, R.D.; Clements, J.; Eddy, S.R. HMMER web server: Interactive sequence similaritysearching. Nucleic Acids Res. 2011, 39, W29-W37.
    • (2011) Nucleic Acids Res , vol.39
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 31
    • 77953633943 scopus 로고    scopus 로고
    • The discovery of zinc fingers and their applications in gene regulation and genomemanipulation
    • Klug, A. The discovery of zinc fingers and their applications in gene regulation and genomemanipulation. Annu. Rev. Biochem. 2010, 79, 213-231.
    • (2010) Annu. Rev. Biochem , vol.79 , pp. 213-231
    • Klug, A.1
  • 32
    • 77958130019 scopus 로고    scopus 로고
    • Rapid sequence and expression divergencesuggests selection for novel function in primate-specific KRAB-ZNF genes
    • Nowick, K.; Hamilton, A.T.; Zhang, H.; Stubbs, L. Rapid sequence and expression divergencesuggests selection for novel function in primate-specific KRAB-ZNF genes. Mol. Biol. Evol. 2010,27, 2606-2617.
    • (2010) Mol. Biol. Evol , vol.27 , pp. 2606-2617
    • Nowick, K.1    Hamilton, A.T.2    Zhang, H.3    Stubbs, L.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.