메뉴 건너뛰기




Volumn 3, Issue 9, 2008, Pages

Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTION FACTOR; UNTRANSLATED RNA; ZINC FINGER PROTEIN;

EID: 52349098749     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003122     Document Type: Article
Times cited : (9)

References (41)
  • 3
    • 43549090410 scopus 로고    scopus 로고
    • Functional protein divergence in the evolution of Homo sapiens
    • Lopez-Bigas N, De S, Teichmann S (2008) Functional protein divergence in the evolution of Homo sapiens. Genome Biology 9: R33.
    • (2008) Genome Biology , vol.9
    • Lopez-Bigas, N.1    De, S.2    Teichmann, S.3
  • 4
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-16.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.C.1    Wilson, A.C.2
  • 5
    • 23244467882 scopus 로고    scopus 로고
    • Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage
    • Ihmels J, Bergmann S, Gerami-Nejad M, Yanai I, McClellan M, et al. (2005) Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage. Science 309: 938-940.
    • (2005) Science , vol.309 , pp. 938-940
    • Ihmels, J.1    Bergmann, S.2    Gerami-Nejad, M.3    Yanai, I.4    McClellan, M.5
  • 6
    • 33751327438 scopus 로고    scopus 로고
    • Comparative Gene Expression Analysis by a Differential Clustering Approach: Application to the Candida albicans Transcription Program
    • Ihmels J, Bergmann S, Berman J, Barkai N (2005) Comparative Gene Expression Analysis by a Differential Clustering Approach: Application to the Candida albicans Transcription Program. PLoS Genet 1: e39.
    • (2005) PLoS Genet , vol.1
    • Ihmels, J.1    Bergmann, S.2    Berman, J.3    Barkai, N.4
  • 8
    • 28844482836 scopus 로고    scopus 로고
    • Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes
    • Lee S, Kohane I, Kasif S (2005) Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. BMC Genomics 6: 168.
    • (2005) BMC Genomics , vol.6 , pp. 168
    • Lee, S.1    Kohane, I.2    Kasif, S.3
  • 9
    • 10344251533 scopus 로고    scopus 로고
    • Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network
    • Iwama H, Gojobori T (2004) Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network. Proceedings of the National Academy of Sciences 101: 17156-17161.
    • (2004) Proceedings of the National Academy of Sciences , vol.101 , pp. 17156-17161
    • Iwama, H.1    Gojobori, T.2
  • 10
    • 33644855479 scopus 로고    scopus 로고
    • Expression profiling in primates reveals a rapid evolution of human transcription factors
    • Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245.
    • (2006) Nature , vol.440 , pp. 242-245
    • Gilad, Y.1    Oshlack, A.2    Smyth, G.K.3    Speed, T.P.4    White, K.P.5
  • 11
    • 33845231723 scopus 로고    scopus 로고
    • Oldham MC, Horvath S, Geschwind DH (2006) Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proceedings of the National Academy of Sciences: 0605938103.
    • Oldham MC, Horvath S, Geschwind DH (2006) Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proceedings of the National Academy of Sciences: 0605938103.
  • 12
    • 4444339460 scopus 로고    scopus 로고
    • Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum
    • Coulson RM, Hall N, Ouzounis CA (2004) Comparative Genomics of Transcriptional Control in the Human Malaria Parasite Plasmodium falciparum. Genome Res 14: 1548-1554.
    • (2004) Genome Res , vol.14 , pp. 1548-1554
    • Coulson, R.M.1    Hall, N.2    Ouzounis, C.A.3
  • 13
    • 38349145774 scopus 로고    scopus 로고
    • Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle
    • Shock J, Fischer K, DeRisi J (2007) Whole-genome analysis of mRNA decay in Plasmodium falciparum reveals a global lengthening of mRNA half-life during the intra-erythrocytic development cycle. Genome Biology 8: R134.
    • (2007) Genome Biology , vol.8
    • Shock, J.1    Fischer, K.2    DeRisi, J.3
  • 14
    • 19944429644 scopus 로고    scopus 로고
    • A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses
    • Hall N, Karras M, Raine JD, Carlton JM, Kooij TWA, et al. (2005) A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses. Science 307: 82-86.
    • (2005) Science , vol.307 , pp. 82-86
    • Hall, N.1    Karras, M.2    Raine, J.D.3    Carlton, J.M.4    Kooij, T.W.A.5
  • 15
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3 [prime] UTRs by comparison of several mammals
    • Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3 [prime] UTRs by comparison of several mammals. Nature 434: 338-345.
    • (2005) Nature , vol.434 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.J.3    Golub, T.R.4    Mootha, V.5
  • 16
    • 24144480800 scopus 로고    scopus 로고
    • The 'permeome' of the malaria parasite: An overview of the membrane transport proteins of Plasmodium falciparum
    • Martin R, Henry R, Abbey J, Clements J, Kirk K (2005) The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum. Genome Biology 6: R26.
    • (2005) Genome Biology , vol.6
    • Martin, R.1    Henry, R.2    Abbey, J.3    Clements, J.4    Kirk, K.5
  • 17
    • 20144389848 scopus 로고    scopus 로고
    • Heterochromatin silencing and locus repositioning linked to regulation of virulence genes in Plasmodium falciparum
    • Duraisingh MT, Voss TS, Marty AJ, Duffy MF, Good RT, et al. (2005) Heterochromatin silencing and locus repositioning linked to regulation of virulence genes in Plasmodium falciparum. Cell 121: 13-24.
    • (2005) Cell , vol.121 , pp. 13-24
    • Duraisingh, M.T.1    Voss, T.S.2    Marty, A.J.3    Duffy, M.F.4    Good, R.T.5
  • 18
    • 33644854445 scopus 로고    scopus 로고
    • Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains
    • Llinás M, Bozdech Z, Wong ED, Adai AT, DeRisi JL (2006) Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains. Nucleic Acids Res 34: 1166-73.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1166-1173
    • Llinás, M.1    Bozdech, Z.2    Wong, E.D.3    Adai, A.T.4    DeRisi, J.L.5
  • 19
    • 38349018723 scopus 로고    scopus 로고
    • On the relation between promoter divergence and gene expression evolution
    • Available:, Accessed 26 June 2008
    • Tirosh I, Weinberger A, Bezalel D, Kaganovich M, Barkai N (2008) On the relation between promoter divergence and gene expression evolution. Mol Syst Biol 4: Available: http://dx.doi.org/10.1038/msb4100198. Accessed 26 June 2008.
    • (2008) Mol Syst Biol , vol.4
    • Tirosh, I.1    Weinberger, A.2    Bezalel, D.3    Kaganovich, M.4    Barkai, N.5
  • 20
    • 31444437901 scopus 로고    scopus 로고
    • Combinatorial gene regulation in Plasmodium falciparum
    • van Noort V, Huynen MA (2006) Combinatorial gene regulation in Plasmodium falciparum. Trends in Genetics 22: 73-78.
    • (2006) Trends in Genetics , vol.22 , pp. 73-78
    • van Noort, V.1    Huynen, M.A.2
  • 21
    • 4243071596 scopus 로고    scopus 로고
    • The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    • Bozdech Z, Llinás M, Pulliam BL, Wong ED, Zhu J, et al. (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1: E5.
    • (2003) PLoS Biol , vol.1
    • Bozdech, Z.1    Llinás, M.2    Pulliam, B.L.3    Wong, E.D.4    Zhu, J.5
  • 23
    • 33644787447 scopus 로고    scopus 로고
    • OrthoMCL-DB: Querying a comprehensive multi-species collection of ortholog groups
    • Chen F, Mackey AJ, Stoeckert CJ, Roos DS (2006) OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucl Acids Res 34: D363-368.
    • (2006) Nucl Acids Res , vol.34
    • Chen, F.1    Mackey, A.J.2    Stoeckert, C.J.3    Roos, D.S.4
  • 24
    • 8744234024 scopus 로고    scopus 로고
    • Global analysis of transcript and protein levels across the Plas-modium falciparum life cycle
    • Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, et al. (2004) Global analysis of transcript and protein levels across the Plas-modium falciparum life cycle. Genome Res 14: 2308-2318.
    • (2004) Genome Res , vol.14 , pp. 2308-2318
    • Le Roch, K.G.1    Johnson, J.R.2    Florens, L.3    Zhou, Y.4    Santrosyan, A.5
  • 25
    • 33845905179 scopus 로고    scopus 로고
    • Genome variation and evolution of the malaria parasite Plasmodium falciparum
    • Jeffares DC, Paln A, Berry A, Cox AV, Stalker J, et al. (2007) Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet 39: 120-125.
    • (2007) Nat Genet , vol.39 , pp. 120-125
    • Jeffares, D.C.1    Paln, A.2    Berry, A.3    Cox, A.V.4    Stalker, J.5
  • 26
    • 23144448511 scopus 로고    scopus 로고
    • Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains
    • Balaji S, Babu MM, Iyer LM, Aravind L (2005) Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucl Acids Res 33: 3994-4006.
    • (2005) Nucl Acids Res , vol.33 , pp. 3994-4006
    • Balaji, S.1    Babu, M.M.2    Iyer, L.M.3    Aravind, L.4
  • 28
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-6.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 30
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-80.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 31
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • Brudno M, Do CB, Cooper GM, Kim MF, Davydov E, et al. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13: 721-31.
    • (2003) Genome Res , vol.13 , pp. 721-731
    • Brudno, M.1    Do, C.B.2    Cooper, G.M.3    Kim, M.F.4    Davydov, E.5
  • 32
    • 34250896139 scopus 로고    scopus 로고
    • Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
    • Vardhanabhuti S, Wang J, Hannenhalli S (2007) Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res 35: 3203-13.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3203-3213
    • Vardhanabhuti, S.1    Wang, J.2    Hannenhalli, S.3
  • 33
    • 0036707816 scopus 로고    scopus 로고
    • Identification of transcription factor binding sites in the human genome sequence
    • Levy S, Hannenhalli S (2002) Identification of transcription factor binding sites in the human genome sequence. Mamm Genome 13: 510-4.
    • (2002) Mamm Genome , vol.13 , pp. 510-514
    • Levy, S.1    Hannenhalli, S.2
  • 34
    • 0037015614 scopus 로고    scopus 로고
    • Genome sequence of the human malaria parasite Plasmodium falciparum
    • Gardner MJ, Hall N, Fung E, White O, Berriman M, et al. (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511.
    • (2002) Nature , vol.419 , pp. 498-511
    • Gardner, M.J.1    Hall, N.2    Fung, E.3    White, O.4    Berriman, M.5
  • 35
    • 0037015592 scopus 로고    scopus 로고
    • Genome sequence and comparative analysis of the-model rodent malaria parasite Plasmodium yoelii yoelii
    • Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, et al. (2002) Genome sequence and comparative analysis of the-model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419: 512-9.
    • (2002) Nature , vol.419 , pp. 512-519
    • Carlton, J.M.1    Angiuoli, S.V.2    Suh, B.B.3    Kooij, T.W.4    Pertea, M.5
  • 36
    • 9144258616 scopus 로고    scopus 로고
    • Protein kinases of the human malaria parasite Plasmodium falciparum: The kinome of a divergent eukaryote
    • Ward P, Equinet L, Packer J, Doerig C (2004) Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics 5: 79.
    • (2004) BMC Genomics , vol.5 , pp. 79
    • Ward, P.1    Equinet, L.2    Packer, J.3    Doerig, C.4
  • 37
    • 16344366882 scopus 로고    scopus 로고
    • In silico gene function prediction using ontology-based pattern identitication
    • Zhou Y, Young JA, Santrosyan A, Chen K, Yan SF, et al. (2005) In silico gene function prediction using ontology-based pattern identitication. Bioinformatics 21: 1237-45.
    • (2005) Bioinformatics , vol.21 , pp. 1237-1245
    • Zhou, Y.1    Young, J.A.2    Santrosyan, A.3    Chen, K.4    Yan, S.F.5
  • 39
    • 0038015442 scopus 로고    scopus 로고
    • Linker scanning mutagenesis of the Plasmodium gallinaceum sexual stage specific gene pgs28 reveals a novel downstream cis-control element
    • Chow CS, Wirth DF (2003) Linker scanning mutagenesis of the Plasmodium gallinaceum sexual stage specific gene pgs28 reveals a novel downstream cis-control element. Molecular and Biochemical Parasitology 129: 199-208.
    • (2003) Molecular and Biochemical Parasitology , vol.129 , pp. 199-208
    • Chow, C.S.1    Wirth, D.F.2
  • 41
    • 0026683042 scopus 로고
    • A sequente element associated with the Plasmodium falciparum KAHRP gene is the site of developmentally regulated protein-DNA interactions
    • Lanzer M, de Bruin D, Ravetch JV (1992) A sequente element associated with the Plasmodium falciparum KAHRP gene is the site of developmentally regulated protein-DNA interactions. Nucl Acids Res 20: 3051-3056.
    • (1992) Nucl Acids Res , vol.20 , pp. 3051-3056
    • Lanzer, M.1    de Bruin, D.2    Ravetch, J.V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.