메뉴 건너뛰기




Volumn 3, Issue , 2003, Pages

Position specific variation in the rate of evolution in transcription factor binding sites

Author keywords

[No Author keywords available]

Indexed keywords

SACCHAROMYCES; SACCHAROMYCES BAYANUS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES MIKATAE; SACCHAROMYCES PARADOXUS; SACCHAROMYCETALES;

EID: 0642368358     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-3-19     Document Type: Article
Times cited : (126)

References (47)
  • 1
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo GD: DNA binding sites: representation and discovery. Bioinformatics 2000, 16(1):16-23.
    • (2000) Bioinformatics , vol.16 , Issue.1 , pp. 16-23
    • Stormo, G.D.1
  • 2
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF and Wootton JC: Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262(5131):208-214.
    • (1993) Science , vol.262 , Issue.5131 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 4
    • 0344376570 scopus 로고    scopus 로고
    • Finding composite regulatory patterns in DNA sequences
    • Eskin E and Pevzner PA: Finding composite regulatory patterns in DNA sequences. Bioinformatics 2002, 18(Suppl 1):S354-363.
    • (2002) Bioinformatics , vol.18 , Issue.1 SUPPL.
    • Eskin, E.1    Pevzner, P.A.2
  • 5
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
    • Liu XS, Brutlag DL and Liu JS: An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat Biotechnol 2002, 20(8):835-839.
    • (2002) Nat Biotechnol , vol.20 , Issue.8 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 6
    • 0033677426 scopus 로고    scopus 로고
    • Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification
    • Marsan L and Sagot MF: Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J Comput Biol 2000, 7(3-4):345-362.
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 345-362
    • Marsan, L.1    Sagot, M.F.2
  • 9
    • 0036106051 scopus 로고    scopus 로고
    • Algorithms for phylogenetic footprinting
    • Blanchette M, Schwikowski B and Tompa : Algorithms for phylogenetic footprinting. J Comput Biol 2002, 9(2):211-223.
    • (2002) J Comput Biol , vol.9 , Issue.2 , pp. 211-223
    • Blanchette, M.1    Schwikowski, B.2    Tompa3
  • 11
    • 0036180002 scopus 로고    scopus 로고
    • The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons
    • Rajewsky N, Socci ND, Zapotocky M and Siggia ED: The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons. Genome Res 2002, 12(2):298-308.
    • (2002) Genome Res , vol.12 , Issue.2 , pp. 298-308
    • Rajewsky, N.1    Socci, N.D.2    Zapotocky, M.3    Siggia, E.D.4
  • 12
    • 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 and Lander ES: Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Elements. Nature 2003, 423(6937):241-254.
    • (2003) Nature , vol.423 , Issue.6937 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 13
    • 0034284481 scopus 로고    scopus 로고
    • Conserved noncoding sequences are reliable guides to regulatory elements
    • Hardison RC: Conserved noncoding sequences are reliable guides to regulatory elements. Trends in Genetics 2000, 16(9):369-372.
    • (2000) Trends in Genetics , vol.16 , Issue.9 , pp. 369-372
    • Hardison, R.C.1
  • 15
    • 0031889035 scopus 로고    scopus 로고
    • Functional analysis of eve stripe 2 enhancer evolution in Drosophila: Rules governing conservation and change
    • Ludwig MZ, Patel NH and Kreitman M: Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. Development 1998, 125(5):949-958.
    • (1998) Development , vol.125 , Issue.5 , pp. 949-958
    • Ludwig, M.Z.1    Patel, N.H.2    Kreitman, M.3
  • 16
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover
    • Dermitzakis ET and Clark AG: Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover. Mol Biol Evol 2002, 19(7):1114-1121.
    • (2002) Mol Biol Evol , vol.19 , Issue.7 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 19
    • 0034783060 scopus 로고    scopus 로고
    • Enrichment of regulatory signals in conserved non-coding genomic sequence
    • Levy S, Hannenhalli S and Workman C: Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics 2001, 17(10):871-877.
    • (2001) Bioinformatics , vol.17 , Issue.10 , pp. 871-877
    • Levy, S.1    Hannenhalli, S.2    Workman, C.3
  • 20
    • 0032861774 scopus 로고    scopus 로고
    • SCPD: A promoter database of the yeast Saccharomyces cerevisiae
    • Zhu J and Zhang MQ: SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 1999, 15(7-8):871-877.
    • (1999) Bioinformatics , vol.15 , Issue.7-8 , pp. 871-877
    • Zhu, J.1    Zhang, M.Q.2
  • 22
    • 0003421005 scopus 로고    scopus 로고
    • Sinauer Associates, Sunderland MA
    • Li WH: Molecular Evolution Sinauer Associates, Sunderland MA; 1997.
    • (1997) Molecular Evolution
    • Li, W.H.1
  • 24
    • 0024294636 scopus 로고
    • Protein-DNA interaction. No code for recognition
    • Matthews BW: Protein-DNA interaction. No code for recognition. Nature 1988, 335(6188):294-295.
    • (1988) Nature , vol.335 , Issue.6188 , pp. 294-295
    • Matthews, B.W.1
  • 25
    • 0029065860 scopus 로고
    • DNA recognition code of transcription factors
    • Suzuki M, Brenner SE, Gerstein M and Yagi N: DNA recognition code of transcription factors. Protein Eng 1995, 8(4):319-328.
    • (1995) Protein Eng , vol.8 , Issue.4 , pp. 319-328
    • Suzuki, M.1    Brenner, S.E.2    Gerstein, M.3    Yagi, N.4
  • 26
    • 0033120215 scopus 로고    scopus 로고
    • Structure-based prediction of DNA target sites by regulatory proteins
    • Kono H and Sarai A: Structure-based prediction of DNA target sites by regulatory proteins. Proteins 1999, 35(1):114-131.
    • (1999) Proteins , vol.35 , Issue.1 , pp. 114-131
    • Kono, H.1    Sarai, A.2
  • 27
    • 0036013781 scopus 로고    scopus 로고
    • Is there a code for protein-DNA recognition? Probab(ilistical)ly
    • Benos PV, Lapedes AS and Stormo GD: Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays 2002, 24(5):466-475.
    • (2002) Bioessays , vol.24 , Issue.5 , pp. 466-475
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 28
    • 0036529540 scopus 로고    scopus 로고
    • Structural analysis of conserved base pairs in protein-DNA complexes
    • Mirny LA and Gelfand MS: Structural analysis of conserved base pairs in protein-DNA complexes. Nucleic Acids Res 2002, 30(7):1704-1711.
    • (2002) Nucleic Acids Res , vol.30 , Issue.7 , pp. 1704-1711
    • Mirny, L.A.1    Gelfand, M.S.2
  • 29
    • 0031875569 scopus 로고    scopus 로고
    • Evolutionary distances for proteincoding sequences: Modelling site-specific residue frequencies
    • Halpern AL and Bruno WJ: Evolutionary distances for proteincoding sequences: modelling site-specific residue frequencies. Mol Biol Evol 1998, 15(7):910-917.
    • (1998) Mol Biol Evol , vol.15 , Issue.7 , pp. 910-917
    • Halpern, A.L.1    Bruno, W.J.2
  • 30
    • 0026547747 scopus 로고
    • DNA recognition by GAL4: Structure of a protein-DNA complex
    • Marmorstein R, Carey M, Ptashne M and Harrison SC: DNA recognition by GAL4: structure of a protein-DNA complex. Nature 1992, 356(6368):408-414.
    • (1992) Nature , vol.356 , Issue.6368 , pp. 408-414
    • Marmorstein, R.1    Carey, M.2    Ptashne, M.3    Harrison, S.C.4
  • 31
    • 0030950532 scopus 로고    scopus 로고
    • DNA-binding specificity of Mcm1: Operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein
    • Acton TB, Zhong H and Vershon AK: DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein. Mol Cell Biol 1997, 17(4):1881-1889.
    • (1997) Mol Cell Biol , vol.17 , Issue.4 , pp. 1881-1889
    • Acton, T.B.1    Zhong, H.2    Vershon, A.K.3
  • 32
    • 0032524123 scopus 로고    scopus 로고
    • Transcriptional cooperativity: Bending over backwards and doing the flip
    • Kerppola TK: Transcriptional cooperativity: bending over backwards and doing the flip. Structure 1998, 6(5):549-554.
    • (1998) Structure , vol.6 , Issue.5 , pp. 549-554
    • Kerppola, T.K.1
  • 33
    • 0032509980 scopus 로고    scopus 로고
    • Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex
    • Tan S and Richmond TJ: Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature 1998, 391(6668):660-666.
    • (1998) Nature , vol.391 , Issue.6668 , pp. 660-666
    • Tan, S.1    Richmond, T.J.2
  • 34
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation
    • Yang Z, Goldman N and Friday AE: Comparison of models for nucleotide substitution used in maximum likelihood phylogenetic estimation. Mol Biol Evol 1994, 11(2):316-324.
    • (1994) Mol Biol Evol , vol.11 , Issue.2 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.E.3
  • 35
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13(5):555-556.
    • (1997) Comput Appl Biosci , vol.13 , Issue.5 , pp. 555-556
    • Yang, Z.1
  • 36
    • 0037163129 scopus 로고    scopus 로고
    • Genome-wide Analysis of Gene Expression Regulated by the Calcineurin/Crz1p Signalling Pathway in Saccharomyces cerevisiae
    • Yoshimoto H, Saltsman K, Gasch AP, Li HX, Ogawa N, Botstein D, Brown PO and Cyert MS: Genome-wide Analysis of Gene Expression Regulated by the Calcineurin/Crz1p Signalling Pathway in Saccharomyces cerevisiae. J Biol Chem 2002, 277(34):31079-31088.
    • (2002) J Biol Chem , vol.277 , Issue.34 , pp. 31079-31088
    • Yoshimoto, H.1    Saltsman, K.2    Gasch, A.P.3    Li, H.X.4    Ogawa, N.5    Botstein, D.6    Brown, P.O.7    Cyert, M.S.8
  • 38
    • 0031153858 scopus 로고    scopus 로고
    • Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA
    • Nielsen R: Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst Biol 1997, 46(2):346-353.
    • (1997) Syst Biol , vol.46 , Issue.2 , pp. 346-353
    • Nielsen, R.1
  • 39
    • 0035999971 scopus 로고    scopus 로고
    • Distribution patterns of over-represented k-mers in non-coding yeast DNA
    • Hampson S, Kibler D and Baldi P: Distribution patterns of over-represented k-mers in non-coding yeast DNA. Bioinformatics 2002, 18(4):513-528.
    • (2002) Bioinformatics , vol.18 , Issue.4 , pp. 513-528
    • Hampson, S.1    Kibler, D.2    Baldi, P.3
  • 40
    • 0031832544 scopus 로고    scopus 로고
    • The Yeast Protein Database (YPD): A curated proteome database for Saccharomyces cerevisiae
    • Hodges PE, Payne WE and Garrels JI: The Yeast Protein Database (YPD): a curated proteome database for Saccharomyces cerevisiae. Nucleic Acids Res 1998, 26(1):68-72.
    • (1998) Nucleic Acids Res , vol.26 , Issue.1 , pp. 68-72
    • Hodges, P.E.1    Payne, W.E.2    Garrels, J.I.3
  • 41
  • 45
    • 0025675724 scopus 로고
    • A maximum likelihood approach to the detection of selection from a phylogeny
    • Golding B and Felsenstein J: A maximum likelihood approach to the detection of selection from a phylogeny. J Mol Evol 1990, 31:511-523.
    • (1990) J Mol Evol , vol.31 , pp. 511-523
    • Golding, B.1    Felsenstein, J.2
  • 46
    • 0000800333 scopus 로고
    • On the probability of fixation of mutant genes in a population
    • Kimura M: On the probability of fixation of mutant genes in a population. Genetics 1962, 4:713-719.
    • (1962) Genetics , vol.4 , pp. 713-719
    • Kimura, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.