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Volumn 2, Issue 1, 2009, Pages 448-469

Structural fingerprints of transcription factor binding site regions

Author keywords

DNA structure; Fourier transform; Sequence dependent structure; Structural fingerprint; Transcription factor binding site

Indexed keywords


EID: 84859092126     PISSN: None     EISSN: 19994893     Source Type: Journal    
DOI: 10.3390/a2010448     Document Type: Article
Times cited : (1)

References (36)
  • 2
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • Collins, F.S., Lander, E.S., Rogers, J. and Waterston, R.H., Finishing the euchromatic sequence of the human genome. Nature 2004, 431, 931-945.
    • (2004) Nature , vol.431 , pp. 931-945
    • Collins, F.S.1    Lander, E.S.2    Rogers, J.3    Waterston, R.H.4
  • 4
    • 0242410740 scopus 로고    scopus 로고
    • Heirlooms in the attic
    • Johnston, M. and Stormo, G.D. Heirlooms in the attic. Science 2003, 302, 997-998.
    • (2003) Science , vol.302 , pp. 997-998
    • Johnston, M.1    Stormo, G.D.2
  • 5
    • 0030863002 scopus 로고    scopus 로고
    • Eukaryotic promoter recognition
    • Fickett, J.W. and Hatzigeorgiou, A.C. Eukaryotic promoter recognition. Genome Res. 1997, 7, 861-878.
    • (1997) Genome Res , vol.7 , pp. 861-878
    • Fickett, J.W.1    Hatzigeorgiou, A.C.2
  • 6
    • 0023043752 scopus 로고
    • A measure of DNA periodicity
    • Silverman, B.D. and Linsker, R. A measure of DNA periodicity. J. Theor. Biol. 1986, 118, 295-300.
    • (1986) J. Theor. Biol. , vol.118 , pp. 295-300
    • Silverman, B.D.1    Linsker, R.2
  • 8
    • 0037202373 scopus 로고    scopus 로고
    • Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis
    • Fukushima, A.; Ikemura, T.; Kinouchi, M.; Oshima, T.; Kudo, Y.; Mori, H. and Kanaya, S. Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis. Gene 2002, 300, 203-211.
    • (2002) Gene , vol.300 , pp. 203-211
    • Fukushima, A.1    Ikemura, T.2    Kinouchi, M.3    Oshima, T.4    Kudo, Y.5    Mori, H.6    Kanaya, S.7
  • 9
    • 0032001783 scopus 로고    scopus 로고
    • 3-, 10.5-, 200- and 400-base periodicities in genome sequences
    • Trifonov, E.N. 3-, 10.5-, 200- and 400-base periodicities in genome sequences. Physica a-Stat. Mech. App. 1998, 249, 511-516.
    • (1998) Physica a-Stat. Mech. App. , vol.249 , pp. 511-516
    • Trifonov, E.N.1
  • 10
    • 0030596486 scopus 로고    scopus 로고
    • Short-range order in two eukaryotic genomes: Relation to chromosome structure
    • Widom, J. Short-range order in two eukaryotic genomes: Relation to chromosome structure. J. Mol. Biol. 1996, 259, 579-588.
    • (1996) J. Mol. Biol. , vol.259 , pp. 579-588
    • Widom, J.1
  • 11
    • 33644643053 scopus 로고    scopus 로고
    • Improved alignment of nucleosome DNA sequences using a mixture model
    • Wang, J.P.Z. and Widom, J. Improved alignment of nucleosome DNA sequences using a mixture model. Nucleic Acids Res. 2005, 33, 6743-6755.
    • (2005) Nucleic Acids Res , vol.33 , pp. 6743-6755
    • Wang, J.P.Z.1    Widom, J.2
  • 12
    • 13944272660 scopus 로고    scopus 로고
    • Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation
    • Dalal, Y.; Fleury, T.J.; Cioffi, A. and Stein, A. Long-range oscillation in a periodic DNA sequence motif may influence nucleosome array formation. Nucleic Acids Res. 2005, 33, 934-945.
    • (2005) Nucleic Acids Res , vol.33 , pp. 934-945
    • Dalal, Y.1    Fleury, T.J.2    Cioffi, A.3    Stein, A.4
  • 13
    • 21444448432 scopus 로고    scopus 로고
    • SWIFT (sequence-wide investigation with Fourier transform): a software tool for identifying proteins of a given class from the unannotated genome sequence
    • D'Avenio, G.; Grigioni, M.; Orefici, G. and Creti, R. SWIFT (sequence-wide investigation with Fourier transform): a software tool for identifying proteins of a given class from the unannotated genome sequence. Bioinf. 2005, 21, 2943-2949.
    • (2005) Bioinf , vol.21 , pp. 2943-2949
    • D'Avenio, G.1    Grigioni, M.2    Orefici, G.3    Creti, R.4
  • 14
    • 3142727129 scopus 로고    scopus 로고
    • Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation
    • Sharma, D.; Issac, B.; Raghava, G.P.S. and Ramaswamy, R. Spectral Repeat Finder (SRF): identification of repetitive sequences using Fourier transformation. Bioinf. 2004, 20, 1405-1412.
    • (2004) Bioinf , vol.20 , pp. 1405-1412
    • Sharma, D.1    Issac, B.2    Raghava, G.P.S.3    Ramaswamy, R.4
  • 16
    • 2442695243 scopus 로고    scopus 로고
    • Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment
    • Dermitzakis, E.T.; Kirkness, E.; Schwarz, S.; Birney, E.; Reymond, A. and Antonarakis, S.E. Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. Genome Res. 2004, 14, 852-859.
    • (2004) Genome Res , vol.14 , pp. 852-859
    • Dermitzakis, E.T.1    Kirkness, E.2    Schwarz, S.3    Birney, E.4    Reymond, A.5    Antonarakis, S.E.6
  • 18
    • 33646252228 scopus 로고    scopus 로고
    • Genomic data analysis using DNA structure: an analysis of Conserved Non-Genic sequences and Ultra-Conserved Elements
    • Gardiner, E.J.; Hirons, L.; Hunter, C.A. and Willett, P. Genomic data analysis using DNA structure: an analysis of Conserved Non-Genic sequences and Ultra-Conserved Elements. J. Chem. Inf. Model. 2006, 46, 753-761.
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 753-761
    • Gardiner, E.J.1    Hirons, L.2    Hunter, C.A.3    Willett, P.4
  • 19
    • 0027318463 scopus 로고
    • Sequence-dependent DNA-structure - the role of base stacking interactions
    • Hunter, C.A. Sequence-dependent DNA-structure - the role of base stacking interactions. J. Mol. Biol. 1993, 230, 1025-1054.
    • (1993) J. Mol. Biol. , vol.230 , pp. 1025-1054
    • Hunter, C.A.1
  • 20
    • 0030919777 scopus 로고    scopus 로고
    • Construction of double-helical DNA structures based on dinucleotide building blocks
    • Hunter, C.A. and Lu, X.J. Construction of double-helical DNA structures based on dinucleotide building blocks. J. Biomol. Struct. Dyn. 1997, 14, 747-756.
    • (1997) J. Biomol. Struct. Dyn. , vol.14 , pp. 747-756
    • Hunter, C.A.1    Lu, X.J.2
  • 21
    • 0031556948 scopus 로고    scopus 로고
    • DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide X-ray crystal structures
    • Hunter, C.A. and Lu, X.J. DNA base-stacking interactions: A comparison of theoretical calculations with oligonucleotide X-ray crystal structures. J. Mol. Biol. 1997, 265, 603-619.
    • (1997) J. Mol. Biol. , vol.265 , pp. 603-619
    • Hunter, C.A.1    Lu, X.J.2
  • 22
    • 0034614483 scopus 로고    scopus 로고
    • Sequence-dependent DNA structure: Dinucleotide conformational maps
    • Packer, M.J.; Dauncey, M.P. and Hunter, C.A. Sequence-dependent DNA structure: Dinucleotide conformational maps. J. Mol. Biol. 2000, 295, 71-83.
    • (2000) J. Mol. Biol. , vol.295 , pp. 71-83
    • Packer, M.J.1    Dauncey, M.P.2    Hunter, C.A.3
  • 23
    • 0034614487 scopus 로고    scopus 로고
    • Sequence-dependent DNA structure: Tetranucleotide conformational maps
    • Packer, M.J.; Dauncey, M.P. and Hunter, C.A. Sequence-dependent DNA structure: Tetranucleotide conformational maps. J. Mol. Biol. 2000, 295, 85-103.
    • (2000) J. Mol. Biol. , vol.295 , pp. 85-103
    • Packer, M.J.1    Dauncey, M.P.2    Hunter, C.A.3
  • 24
    • 0034823069 scopus 로고    scopus 로고
    • Sequence-structure relationships in DNA oligomers: A computational approach
    • Packer, M.J. and Hunter, C.A. Sequence-structure relationships in DNA oligomers: A computational approach. J. Am. Chem. Soc. 2001, 123, 7399-7406.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 7399-7406
    • Packer, M.J.1    Hunter, C.A.2
  • 25
    • 5144232010 scopus 로고    scopus 로고
    • A structural similarity analysis of doublehelical DNA
    • Gardiner, E.J.; Hunter, C.A.; Lu, X.J. and Willett, P. A structural similarity analysis of doublehelical DNA. J. Mol. Biol. 2004, 343, 879-889.
    • (2004) J. Mol. Biol. , vol.343 , pp. 879-889
    • Gardiner, E.J.1    Hunter, C.A.2    Lu, X.J.3    Willett, P.4
  • 26
    • 0042386600 scopus 로고    scopus 로고
    • Sequence-dependent DNA structure: A database of octamer structural parameters
    • Gardiner, E.J.; Hunter, C.A.; Packer, M.J.; Palmer, D.S. and Willett, P. Sequence-dependent DNA structure: A database of octamer structural parameters. J. Mol. Biol. 2003, 332, 1025-1035.
    • (2003) J. Mol. Biol. , vol.332 , pp. 1025-1035
    • Gardiner, E.J.1    Hunter, C.A.2    Packer, M.J.3    Palmer, D.S.4    Willett, P.5
  • 27
    • 33645777446 scopus 로고    scopus 로고
    • CpG island methylation in human lymphocytes is highly correlated with DNA sequence patters, repeat frequencies and predicted DNA structure
    • Bock, C.; Paulsen, M.; Tierling, S.; Mikesa, T.; Lengauer, T. and Walter, J. CpG island methylation in human lymphocytes is highly correlated with DNA sequence patters, repeat frequencies and predicted DNA structure. PLoS Genetics 2006, 2, 243-252.
    • (2006) PLoS Genetics , vol.2 , pp. 243-252
    • Bock, C.1    Paulsen, M.2    Tierling, S.3    Mikesa, T.4    Lengauer, T.5    Walter, J.6
  • 28
    • 0027059264 scopus 로고
    • Assessment of protein coding measures
    • Fickett, J.W. and Tung, C.S. Assessment of protein coding measures. Nucleic Acids Res. 1992, 20, 6441-6450.
    • (1992) Nucleic Acids Res , vol.20 , pp. 6441-6450
    • Fickett, J.W.1    Tung, C.S.2
  • 33
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • Kent, W.J. BLAT - The BLAST-like alignment tool. Genome Res. 2002, 12, 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 34
    • 0033669056 scopus 로고    scopus 로고
    • Combination of molecular similarity measures using data fusion
    • Ginn, C.M.R.; Willett, P. and Bradshaw, J. Combination of molecular similarity measures using data fusion. Perspect. Drug Discov. Des. 2000, 20, 1-16.
    • (2000) Perspect. Drug Discov. Des. , vol.20 , pp. 1-16
    • Ginn, C.M.R.1    Willett, P.2    Bradshaw, J.3
  • 35
    • 0037361941 scopus 로고    scopus 로고
    • Combination of fingerprint-based similarity coefficients using data fusion
    • Salim, N.; Holliday, J. and Willett, P. Combination of fingerprint-based similarity coefficients using data fusion. J. Chem. Inf. Comput. Sci. 2003, 43, 435-442.
    • (2003) J. Chem. Inf. Comput. Sci. , vol.43 , pp. 435-442
    • Salim, N.1    Holliday, J.2    Willett, P.3
  • 36
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • Charifson, P.S.; Corkery, J.J.; Murcko, M.A. and Walters, W.P. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 1999, 42, 5100-5109.
    • (1999) J. Med. Chem. , vol.42 , pp. 5100-5109
    • Charifson, P.S.1    Corkery, J.J.2    Murcko, M.A.3    Walters, W.P.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.