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Volumn 5, Issue 2, 2010, Pages

The effect of orthology and coregulation on detecting regulatory motifs

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; FUNGAL PROTEIN; LEXA PROTEIN; RAP1 PROTEIN; TRANSCRIPTION FACTOR; TYRR PROTEIN; UNCLASSIFIED DRUG; URS1H PROTEIN;

EID: 77949367876     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008938     Document Type: Article
Times cited : (5)

References (34)
  • 3
    • 11144354360 scopus 로고    scopus 로고
    • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
    • Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
  • 4
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif finding algorithms
    • Das MK, Dai HK (2007) A survey of DNA motif finding algorithms. BMC Bioinformatics 8 Suppl 7: S21.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 7
    • Das, M.K.1    Dai, H.K.2
  • 6
    • 10344266395 scopus 로고    scopus 로고
    • In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection
    • Marchal K, De Keersmaecker S, Monsieurs P, van Boxel N, Lemmens K, et al. (2004) In silico identification and experimental validation of PmrAB targets in Salmonella typhimurium by regulatory motif detection. Genome Biol 5: R9.
    • (2004) Genome Biol , vol.5
    • Marchal, K.1    De Keersmaecker, S.2    Monsieurs, P.3    van Boxel, N.4    Lemmens, K.5
  • 7
    • 1542376789 scopus 로고    scopus 로고
    • Eukaryotic regulatory element conservation analysis and identification using comparative genomics
    • Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S (2004) Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res 14: 451-458.
    • (2004) Genome Res , vol.14 , pp. 451-458
    • Liu, Y.1    Liu, X.S.2    Wei, L.3    Altman, R.B.4    Batzoglou, S.5
  • 8
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 9
    • 0344906814 scopus 로고    scopus 로고
    • Combining phylogenetic data with co-regulated genes to identify regulatory motifs
    • Wang T, Stormo GD (2003) Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 19: 2369-2380.
    • (2003) Bioinformatics , vol.19 , pp. 2369-2380
    • Wang, T.1    Stormo, G.D.2
  • 10
    • 0034919548 scopus 로고    scopus 로고
    • Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis
    • Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, et al. (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 11: 1175-1186.
    • (2001) Genome Res , vol.11 , pp. 1175-1186
    • Cliften, P.F.1    Hillier, L.W.2    Fulton, L.3    Graves, T.4    Miner, T.5
  • 11
    • 0034141782 scopus 로고    scopus 로고
    • Prediction of transcription regulatory sites in Archaea by a comparative genomic approach
    • Gelfand MS, Koonin EV, Mironov AA (2000) Prediction of transcription regulatory sites in Archaea by a comparative genomic approach. Nucleic Acids Res 28: 695-705.
    • (2000) Nucleic Acids Res , vol.28 , pp. 695-705
    • Gelfand, M.S.1    Koonin, E.V.2    Mironov, A.A.3
  • 12
    • 0033918228 scopus 로고    scopus 로고
    • Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes
    • McGuire AM, Hughes JD, Church GM (2000) Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res 10: 744-757.
    • (2000) Genome Res , vol.10 , pp. 744-757
    • McGuire, A.M.1    Hughes, J.D.2    Church, G.M.3
  • 13
    • 0036107903 scopus 로고    scopus 로고
    • Discovery of regulatory elements by a computational method for phylogenetic footprinting
    • Blanchette M, Tompa M (2002) Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res 12: 739-748.
    • (2002) Genome Res , vol.12 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 14
    • 2442693190 scopus 로고    scopus 로고
    • Phylogenetic motif detection by expectation-maximization on evolutionary mixtures
    • Moses AM, Chiang DY, Eisen MB (2004) Phylogenetic motif detection by expectation-maximization on evolutionary mixtures. Pac Symp Biocomput. pp 324-335.
    • (2004) Pac Symp Biocomput , pp. 324-335
    • Moses, A.M.1    Chiang, D.Y.2    Eisen, M.B.3
  • 16
    • 13244260826 scopus 로고    scopus 로고
    • PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
    • Sinha S, Blanchette M, Tompa M (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics 5: 170.
    • (2004) BMC Bioinformatics , vol.5 , pp. 170
    • Sinha, S.1    Blanchette, M.2    Tompa, M.3
  • 17
    • 22144486916 scopus 로고    scopus 로고
    • Sampling motifs on phylogenetic trees
    • Li X, Wong WH (2005) Sampling motifs on phylogenetic trees. Proc Natl Acad Sci U S A 102: 9481-9486.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 9481-9486
    • Li, X.1    Wong, W.H.2
  • 18
    • 33750218960 scopus 로고    scopus 로고
    • PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny
    • Siddharthan R, Siggia ED, van Nimwegen E (2005) PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol 1: e67.
    • (2005) PLoS Comput Biol , vol.1
    • Siddharthan, R.1    Siggia, E.D.2    van Nimwegen, E.3
  • 19
    • 34548139032 scopus 로고    scopus 로고
    • Tree Gibbs Sampler: Identifying conserved motifs without aligning orthologous sequences
    • Cai X, Hu H, Li XS (2007) Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences. Bioinformatics 23: 2013-2014.
    • (2007) Bioinformatics , vol.23 , pp. 2013-2014
    • Cai, X.1    Hu, H.2    Li, X.S.3
  • 20
    • 34547876110 scopus 로고    scopus 로고
    • A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction
    • Newberg LA, Thompson WA, Conlan S, Smith TM, McCue LA, et al. (2007) A phylogenetic Gibbs sampler that yields centroid solutions for cis-regulatory site prediction. Bioinformatics 23: 1718-1727.
    • (2007) Bioinformatics , vol.23 , pp. 1718-1727
    • Newberg, L.A.1    Thompson, W.A.2    Conlan, S.3    Smith, T.M.4    McCue, L.A.5
  • 21
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2: 28-36.
    • (1994) Proc Int Conf Intell Syst Mol Biol , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 22
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern B (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 15: 211-218.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 23
  • 24
    • 0000732090 scopus 로고
    • Evolution of protein molecules
    • New York: Academic Press. pp
    • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Mammalian protein metabolism. New York: Academic Press. pp 21-132.
    • (1969) Mammalian protein metabolism , pp. 21-132
    • Jukes, T.H.1    Cantor, C.R.2
  • 25
    • 1042264827 scopus 로고    scopus 로고
    • Sinha S, van Nimwegen E, Siggia ED (2003) A probabilistic method to detect regulatory modules. Bioinformatics 19 Suppl 1:I292-I301.: I292-I301.
    • Sinha S, van Nimwegen E, Siggia ED (2003) A probabilistic method to detect regulatory modules. Bioinformatics 19 Suppl 1:I292-I301.: I292-I301.
  • 26
    • 0036191009 scopus 로고    scopus 로고
    • INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling
    • Thijs G, Moreau Y, De Smet F, Mathys J, Lescot M, et al. (2002) INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling. Bioinformatics 18: 331-332.
    • (2002) Bioinformatics , vol.18 , pp. 331-332
    • Thijs, G.1    Moreau, Y.2    De Smet, F.3    Mathys, J.4    Lescot, M.5
  • 27
    • 0004182828 scopus 로고    scopus 로고
    • Monte Carlo Strategies in Scientific Computing
    • 360 p
    • Liu JS (2001) Monte Carlo Strategies in Scientific Computing. Springer Series in Statistics. 360 p.
    • (2001) Springer Series in Statistics
    • Liu, J.S.1
  • 29
    • 18844374522 scopus 로고    scopus 로고
    • Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
    • Tanay A, Regev A, Shamir R (2005) Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci US A 102: 7203-7208.
    • (2005) Proc Natl Acad Sci US A , vol.102 , pp. 7203-7208
    • Tanay, A.1    Regev, A.2    Shamir, R.3
  • 30
    • 67650601963 scopus 로고    scopus 로고
    • Evolution of transcriptional regulatory circuits in bacteria
    • Perez JC, Groisman EA (2009) Evolution of transcriptional regulatory circuits in bacteria. Cell 138: 233-244.
    • (2009) Cell , vol.138 , pp. 233-244
    • Perez, J.C.1    Groisman, E.A.2
  • 32
    • 34249681307 scopus 로고    scopus 로고
    • Binding site graphs: A new graph theoretical framework for prediction of transcription factor binding sites
    • Reddy TE, DeLisi C, Shakhnovich BE (2007) Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites. PLoS Comput Biol 3: e90.
    • (2007) PLoS Comput Biol , vol.3
    • Reddy, T.E.1    DeLisi, C.2    Shakhnovich, B.E.3
  • 33
    • 0034919602 scopus 로고    scopus 로고
    • Identifying functional elements by comparative DNA sequence analysis
    • Tompa M (2001) Identifying functional elements by comparative DNA sequence analysis. Genome Res 11: 1143-1144.
    • (2001) Genome Res , vol.11 , pp. 1143-1144
    • Tompa, M.1
  • 34
    • 46249087629 scopus 로고    scopus 로고
    • Ray P, Shringarpure S, Kolar M, Xing EP (2008) CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. PLoS Comput Biol 4: e1000090.
    • Ray P, Shringarpure S, Kolar M, Xing EP (2008) CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. PLoS Comput Biol 4: e1000090.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.