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Volumn 11, Issue 1, 2010, Pages

Most transcription factor binding sites are in a few mosaic classes of the human genome

Author keywords

[No Author keywords available]

Indexed keywords

GA BINDING PROTEIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MAX PROTEIN; PROTEIN C FOS; PROTEIN P53; STAT1 PROTEIN; STEROL REGULATORY ELEMENT BINDING PROTEIN 1; TRANCRIPTION FACTOR NRSF; TRANCRIPTION FACTOR SRF; TRANCRIPTION FACTOR TR4; TRANCRIPTION FACTOR ZNF263; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR 7 LIKE 2; TRANSCRIPTION FACTOR GATA 1; TRANSCRIPTION FACTOR JUND; TRANSCRIPTION FACTOR NF E2; TRANSCRIPTION FACTOR SP1; TRANSCRIPTION FACTOR YY1; UNCLASSIFIED DRUG;

EID: 77951872802     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-286     Document Type: Article
Times cited : (1)

References (50)
  • 1
    • 34250305146 scopus 로고    scopus 로고
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    • 10.1038/nature05874, 2212820, 17571346, The ENCODE Project Consortium
    • The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. 10.1038/nature05874, 2212820, 17571346, The ENCODE Project Consortium.
    • (2007) Nature , vol.447 , pp. 799-816
  • 3
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif finding algorithms
    • 10.1186/1471-2105-8-S7-S21, 2099490, 18047721
    • Das MK, Dai HK. A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8(Suppl 7):S21. 10.1186/1471-2105-8-S7-S21, 2099490, 18047721.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 7
    • Das, M.K.1    Dai, H.K.2
  • 4
    • 34547540506 scopus 로고    scopus 로고
    • Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting
    • 10.1073/pnas.0701614104, 1851073, 17395715
    • Sosinsky A, Honig B, Mann RS, Califano A. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci USA 2007, 104:6305-6310. 10.1073/pnas.0701614104, 1851073, 17395715.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 6305-6310
    • Sosinsky, A.1    Honig, B.2    Mann, R.S.3    Califano, A.4
  • 5
    • 0036107903 scopus 로고    scopus 로고
    • Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting
    • 10.1101/gr.6902, 186562, 11997340
    • Blanchette M, Tompa M. Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting. Genome Res 2002, 12:739-748. 10.1101/gr.6902, 186562, 11997340.
    • (2002) Genome Res , vol.12 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 6
    • 0027968068 scopus 로고
    • CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 10.1093/nar/22.22.4673, 308517, 7984417
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 8
    • 34347339593 scopus 로고    scopus 로고
    • Improved benchmarks for computational motif discovery
    • 10.1186/1471-2105-8-193, 1903367, 17559676
    • Sandve GK, Abul O, Walseng V, Drabls F. Improved benchmarks for computational motif discovery. BMC Bioinformatics 2007, 8:193. 10.1186/1471-2105-8-193, 1903367, 17559676.
    • (2007) BMC Bioinformatics , vol.8 , pp. 193
    • Sandve, G.K.1    Abul, O.2    Walseng, V.3    Drabls, F.4
  • 9
    • 3242884167 scopus 로고    scopus 로고
    • Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    • 10.1093/nar/gkh465, 441603, 15215380
    • Pavesi G, Mereghetti P, Mauri G, Pesole G. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res 2004, 32:W199-203. 10.1093/nar/gkh465, 441603, 15215380.
    • (2004) Nucleic Acids Res , vol.32
    • Pavesi, G.1    Mereghetti, P.2    Mauri, G.3    Pesole, G.4
  • 10
    • 33747823564 scopus 로고    scopus 로고
    • Meme: discovering and analyzing DNA and protein sequence motifs
    • 10.1093/nar/gkl198, 1538909, 16845028
    • Bailey TL, Williams N, Misleh C, Li WW. Meme: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34:W369-W373. 10.1093/nar/gkl198, 1538909, 16845028.
    • (2006) Nucleic Acids Res , vol.34
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 11
    • 0000097141 scopus 로고    scopus 로고
    • ANN-SPEC: A method for discovering transcription factor binding sites with improved specificity
    • Workman CT, Stormo GD. ANN-SPEC: A method for discovering transcription factor binding sites with improved specificity. Pacific Symposium on Biocomputing 2000, 5:464-475.
    • (2000) Pacific Symposium on Biocomputing , vol.5 , pp. 464-475
    • Workman, C.T.1    Stormo, G.D.2
  • 12
    • 36949006682 scopus 로고    scopus 로고
    • MORPH: Probabilistic alignment combined wih hidden Markov models of cis-regulatory modules
    • Sinha S, He X. MORPH: Probabilistic alignment combined wih hidden Markov models of cis-regulatory modules. PLOS Computational Biology 2007, 11:e216.
    • (2007) PLOS Computational Biology , vol.11
    • Sinha, S.1    He, X.2
  • 13
    • 1242264319 scopus 로고    scopus 로고
    • Finding functional sequence elements by multiple local alignment
    • 10.1093/nar/gkh169, 373279, 14704356
    • Frith MC, Hansen U, Spouge JL, Weng Z. Finding functional sequence elements by multiple local alignment. Nucleic Acids Res 2004, 32:189-200. 10.1093/nar/gkh169, 373279, 14704356.
    • (2004) Nucleic Acids Res , vol.32 , pp. 189-200
    • Frith, M.C.1    Hansen, U.2    Spouge, J.L.3    Weng, Z.4
  • 14
    • 2942517992 scopus 로고    scopus 로고
    • Statistical extraction of Droophila cis-regulatory modules using exhaustive assessment of local word frequency
    • 10.1186/1471-2105-4-65, 341902, 14690551
    • Nazina AG, Papatsenko DA. Statistical extraction of Droophila cis-regulatory modules using exhaustive assessment of local word frequency. BMC Bioinformatics 2003, 4:65. 10.1186/1471-2105-4-65, 341902, 14690551.
    • (2003) BMC Bioinformatics , vol.4 , pp. 65
    • Nazina, A.G.1    Papatsenko, D.A.2
  • 15
    • 25444528967 scopus 로고    scopus 로고
    • Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test
    • 10.1186/1471-2105-6-109, 1127108, 15857505
    • Abnizova I, te Boekhorst R, Walter K, Gilks WR. Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test. BMC Bioinformatics 2005, 6:109. 10.1186/1471-2105-6-109, 1127108, 15857505.
    • (2005) BMC Bioinformatics , vol.6 , pp. 109
    • Abnizova, I.1    te Boekhorst, R.2    Walter, K.3    Gilks, W.R.4
  • 18
    • 68149108057 scopus 로고    scopus 로고
    • Using DNA mechanics to predict in vitro nucleosome positions and formation energies
    • 10.1093/nar/gkp475, 2724288, 19509309
    • Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED. Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res 2009, 37:4707-4722. 10.1093/nar/gkp475, 2724288, 19509309.
    • (2009) Nucleic Acids Res , vol.37 , pp. 4707-4722
    • Morozov, A.V.1    Fortney, K.2    Gaykalova, D.A.3    Studitsky, V.M.4    Widom, J.5    Siggia, E.D.6
  • 19
    • 66349101154 scopus 로고    scopus 로고
    • Predicting functionality of protein-DNA interactions by integrating diverse evidence
    • 10.1093/bioinformatics/btp213, 2687967, 19477979
    • Ucar D, Beyer A, Parthasarathy S, Workman CT. Predicting functionality of protein-DNA interactions by integrating diverse evidence. Bioinformatics 2009, 25:i137-i144. 10.1093/bioinformatics/btp213, 2687967, 19477979.
    • (2009) Bioinformatics , vol.25
    • Ucar, D.1    Beyer, A.2    Parthasarathy, S.3    Workman, C.T.4
  • 20
    • 0344906814 scopus 로고    scopus 로고
    • Combining phylogenetic data with co-regulated genes to identify regulatory motifs
    • 10.1093/bioinformatics/btg329, 14668220
    • Wang T, Stormo GD. Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics 2003, 19:2369-2380. 10.1093/bioinformatics/btg329, 14668220.
    • (2003) Bioinformatics , vol.19 , pp. 2369-2380
    • Wang, T.1    Stormo, G.D.2
  • 21
    • 33750218960 scopus 로고    scopus 로고
    • PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny
    • 10.1371/journal.pcbi.0010067, 1309704,1309704, 16477324
    • Siddharthan R, vNE Siggia ED. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol 2005, 1:e67. 10.1371/journal.pcbi.0010067, 1309704,1309704, 16477324.
    • (2005) PLoS Comput Biol , vol.1
    • Siddharthan, R.1    vNE Siggia, E.D.2
  • 23
    • 35748971744 scopus 로고    scopus 로고
    • DPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
    • 10.1093/bioinformatics/btm288, 17550915
    • Bae SH, Tang H, Wu J, Xie J, Kim S. dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis. Bioinformatics 2007, 23:2619-2621. 10.1093/bioinformatics/btm288, 17550915.
    • (2007) Bioinformatics , vol.23 , pp. 2619-2621
    • Bae, S.H.1    Tang, H.2    Wu, J.3    Xie, J.4    Kim, S.5
  • 24
    • 40549106454 scopus 로고    scopus 로고
    • Effective transription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
    • 10.1186/1471-2105-8-481, 2265442, 18093302
    • Levitsky VG, Ignatieva EV, Ananko EA, Turnaev II, Merkulova TI, Kolchanov NA, Hodgman TC. Effective transription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC bioinformatics 2007, 8:481. 10.1186/1471-2105-8-481, 2265442, 18093302.
    • (2007) BMC bioinformatics , vol.8 , pp. 481
    • Levitsky, V.G.1    Ignatieva, E.V.2    Ananko, E.A.3    Turnaev, I.I.4    Merkulova, T.I.5    Kolchanov, N.A.6    Hodgman, T.C.7
  • 25
    • 14944363825 scopus 로고    scopus 로고
    • NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence
    • 10.1093/nar/gki282, 1064142, 15760844
    • Down TA, Hubbard TJ. NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res 2005, 33:1445-1453. 10.1093/nar/gki282, 1064142, 15760844.
    • (2005) Nucleic Acids Res , vol.33 , pp. 1445-1453
    • Down, T.A.1    Hubbard, T.J.2
  • 26
    • 0026631005 scopus 로고
    • The influence of nearest neighbors on the rate and pattern of spontaneous point mutations
    • 10.1007/BF00162968, 1588594
    • Blake RD, Hess ST, Nicholson-Tuell J. The influence of nearest neighbors on the rate and pattern of spontaneous point mutations. J Mol Evol 1992, 34:189-200. 10.1007/BF00162968, 1588594.
    • (1992) J Mol Evol , vol.34 , pp. 189-200
    • Blake, R.D.1    Hess, S.T.2    Nicholson-Tuell, J.3
  • 27
    • 0028294455 scopus 로고
    • Wide variations in neighbor-dependent substitution rates
    • 10.1016/0022-2836(94)90009-4, 8120884
    • Hess ST, Blake JD, Blake RD. Wide variations in neighbor-dependent substitution rates. J Mol Biol 1994, 236:1022-1033. 10.1016/0022-2836(94)90009-4, 8120884.
    • (1994) J Mol Biol , vol.236 , pp. 1022-1033
    • Hess, S.T.1    Blake, J.D.2    Blake, R.D.3
  • 28
    • 4644300141 scopus 로고    scopus 로고
    • Bayesian Markov Chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
    • 10.1073/pnas.0404142101, 521089, 15292512
    • Hwang DG, Green P. Bayesian Markov Chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA 2004, 101:13994-14001. 10.1073/pnas.0404142101, 521089, 15292512.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 13994-14001
    • Hwang, D.G.1    Green, P.2
  • 29
    • 0036396542 scopus 로고    scopus 로고
    • Rationalization of Gene Regulation by a Eukaryotic Transcription Factor: Calculation of Regulatory Region Occupancy from Predicted Binding Affinities
    • 10.1016/S0022-2836(02)00894-X, 12368093
    • Liu X, Clarke ND. Rationalization of Gene Regulation by a Eukaryotic Transcription Factor: Calculation of Regulatory Region Occupancy from Predicted Binding Affinities. Journal of Molecular Biology 2002, 323:1-8. 10.1016/S0022-2836(02)00894-X, 12368093.
    • (2002) Journal of Molecular Biology , vol.323 , pp. 1-8
    • Liu, X.1    Clarke, N.D.2
  • 30
    • 2942582468 scopus 로고    scopus 로고
    • Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
    • 10.1186/1471-2105-5-31, 407845, 15113405
    • Gao F, Foat BC, Bussemaker HJ. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 2004, 5:31. 10.1186/1471-2105-5-31, 407845, 15113405.
    • (2004) BMC Bioinformatics , vol.5 , pp. 31
    • Gao, F.1    Foat, B.C.2    Bussemaker, H.J.3
  • 31
    • 0014302250 scopus 로고
    • Separation of B. subtilis DNA into complementary strands. III. Direct Analysis
    • 10.1073/pnas.60.3.921, 225140, 4970114
    • Rudner R, Karkas JD, Chargaff E. Separation of B. subtilis DNA into complementary strands. III. Direct Analysis. Proc Natl Acad Sci USA 1968, 60:921-922. 10.1073/pnas.60.3.921, 225140, 4970114.
    • (1968) Proc Natl Acad Sci USA , vol.60 , pp. 921-922
    • Rudner, R.1    Karkas, J.D.2    Chargaff, E.3
  • 32
    • 0033935187 scopus 로고    scopus 로고
    • The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes
    • Tillier ER, Collins RA. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes. J Mol Evol 2000, 50:249-257.
    • (2000) J Mol Evol , vol.50 , pp. 249-257
    • Tillier, E.R.1    Collins, R.A.2
  • 33
    • 40749157998 scopus 로고    scopus 로고
    • Genomic DNA from animals shows contrasting strand bias in large and small subsequences
    • 10.1186/1471-2164-9-43, 2267173, 18221531
    • Evans KJ. Genomic DNA from animals shows contrasting strand bias in large and small subsequences. BMC Genomics 2008, 9:43. 10.1186/1471-2164-9-43, 2267173, 18221531.
    • (2008) BMC Genomics , vol.9 , pp. 43
    • Evans, K.J.1
  • 34
    • 34548396264 scopus 로고    scopus 로고
    • Human Gene organization driven by the coordination of replication and transcription
    • 10.1101/gr.6533407, 1950896, 17675363
    • Huvet M, Nicolay S, Touchon M, Audit B, d'Aubenton-Carafa Y, Arneodo A, Thermes C. Human Gene organization driven by the coordination of replication and transcription. Genome Res 2007, 17:1278-1285. 10.1101/gr.6533407, 1950896, 17675363.
    • (2007) Genome Res , vol.17 , pp. 1278-1285
    • Huvet, M.1    Nicolay, S.2    Touchon, M.3    Audit, B.4    d'Aubenton-Carafa, Y.5    Arneodo, A.6    Thermes, C.7
  • 35
    • 40749122940 scopus 로고    scopus 로고
    • Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression
    • 10.1186/1471-2164-9-16, 2266913, 18194530
    • Evans KJ. Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression. BMC Genomics 2008, 9:16. 10.1186/1471-2164-9-16, 2266913, 18194530.
    • (2008) BMC Genomics , vol.9 , pp. 16
    • Evans, K.J.1
  • 36
    • 65349122997 scopus 로고    scopus 로고
    • Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries
    • 10.1371/journal.pone.0005241, 2666154, 19367334
    • Vega VB, Cheung E, Palanisamy N, Sung WK. Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PloS One 2009, 4:e5241. 10.1371/journal.pone.0005241, 2666154, 19367334.
    • (2009) PloS One , vol.4
    • Vega, V.B.1    Cheung, E.2    Palanisamy, N.3    Sung, W.K.4
  • 40
    • 33947201809 scopus 로고    scopus 로고
    • Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome
    • 10.1016/j.cell.2006.12.048, 2572726, 17382889
    • Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 2007, 128:1231-1245. 10.1016/j.cell.2006.12.048, 2572726, 17382889.
    • (2007) Cell , vol.128 , pp. 1231-1245
    • Kim, T.H.1    Abdullaev, Z.K.2    Smith, A.D.3    Ching, K.A.4    Loukinov, D.I.5    Green, R.D.6    Zhang, M.Q.7    Lobanenkov, V.V.8    Ren, B.9
  • 42
    • 33746691336 scopus 로고    scopus 로고
    • Extensive low-affinity transcriptional interactions in the yeast genome
    • [Tanay, Amos United States Genome research Genome Res. 2006 Aug;16(8):962-72. Epub 2006 Jun 29.], 10.1101/gr.5113606, 1524868, 16809671
    • Tanay A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 2006, 16(8):962-72. [Tanay, Amos United States Genome research Genome Res. 2006 Aug;16(8):962-72. Epub 2006 Jun 29.], 10.1101/gr.5113606, 1524868, 16809671.
    • (2006) Genome Res , vol.16 , Issue.8 , pp. 962-972
    • Tanay, A.1
  • 48
    • 24944555175 scopus 로고    scopus 로고
    • RepeatMasker Open-3.0
    • Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996, , http://www.repeatmasker.org
    • (1996)
    • Smit, A.F.A.1    Hubley, R.2    Green, P.3
  • 50
    • 2142738304 scopus 로고    scopus 로고
    • WebLogo: A sequence logo generator
    • 10.1101/gr.849004, 419797, 15173120
    • Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator. Genome Research 2004, 14:1188-1190. 10.1101/gr.849004, 419797, 15173120.
    • (2004) Genome Research , vol.14 , pp. 1188-1190
    • Crooks, G.E.1    Hon, G.2    Chandonia, J.M.3    Brenner, S.E.4


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