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Volumn 40, Issue 7, 2012, Pages

Use of ChIP-Seq data for the design of a multiple promoter-alignment method

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; TRANSCRIPTION FACTOR;

EID: 84860197189     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1292     Document Type: Article
Times cited : (21)

References (47)
  • 1
    • 68949213578 scopus 로고    scopus 로고
    • Insights from genomic profiling of transcription factors
    • Farnham, P.J. (2009) Insights from genomic profiling of transcription factors. Nat. Rev. Genet., 10, 605-616.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 605-616
    • Farnham, P.J.1
  • 2
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • DOI 10.1038/nature01644
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B. and Lander, E.S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254. (Pubitemid 40852689)
    • (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
  • 3
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
    • DOI 10.1038/nature03441
    • Xie, X., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S. and Kellis, M. (2005) Systematic discovery of regulatory motifs in human promoters and 30 UTRs by comparison of several mammals. Nature, 434, 338-345. (Pubitemid 40469170)
    • (2005) Nature , vol.434 , Issue.7031 , pp. 338-345
    • Xie, X.1    Lu, J.2    Kulbokas, E.J.3    Golub, T.R.4    Mootha, V.5    Lindblad-Toh, K.6    Lander, E.S.7    Kellis, M.8
  • 5
    • 1842679836 scopus 로고    scopus 로고
    • Surveying phylogenetic footprints in large gene clusters: Applications to Hox cluster duplications
    • DOI 10.1016/j.ympev.2003.08.009
    • Prohaska, S.J., Fried, C., Flamm, C., Wagner, G.P. and Stadler, P.F. (2004) Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications. Mol. Phylogenet. Evol., 31, 581-604. (Pubitemid 38504450)
    • (2004) Molecular Phylogenetics and Evolution , vol.31 , Issue.2 , pp. 581-604
    • Prohaska, S.J.1    Fried, C.2    Flamm, C.3    Wagner, G.P.4    Stadler, P.F.5
  • 6
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz, G.Z. and Stormo, G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577. (Pubitemid 29462105)
    • (1999) Bioinformatics , vol.15 , Issue.7-8 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 7
    • 34249808513 scopus 로고    scopus 로고
    • Multiple non-collinear TF-map alignments of promoter regions
    • Blanco, E., Guigo, R. and Messeguer, X. (2007) Multiple non-collinear TF-map alignments of promoter regions. BMC Bioinformatics, 8, 138.
    • (2007) BMC Bioinformatics , vol.8 , pp. 138
    • Blanco, E.1    Guigo, R.2    Messeguer, X.3
  • 8
    • 0345874725 scopus 로고    scopus 로고
    • CORNEAL: Conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting
    • DOI 10.1101/gr.1642804
    • Berezikov, E., Guryev, V., Plasterk, R.H. and Cuppen, E. (2004) CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res., 14, 170-178. (Pubitemid 38088538)
    • (2004) Genome Research , vol.14 , Issue.1 , pp. 170-178
    • Berezikov, E.1    Guryev, V.2    Plasterk, R.H.A.3    Cuppen, E.4
  • 9
    • 36549090457 scopus 로고    scopus 로고
    • Mulan: Multiple-sequence alignment to predict functional elements in genomic sequences
    • Loots, G.G. and Ovcharenko, I. (2007) Mulan: multiple-sequence alignment to predict functional elements in genomic sequences. Methods Mol. Biol., 395, 237-254.
    • (2007) Methods Mol. Biol. , vol.395 , pp. 237-254
    • Loots, G.G.1    Ovcharenko, I.2
  • 11
    • 84860194305 scopus 로고    scopus 로고
    • Measuring transcription factor-binding site turnover: A maximum likelihood approach using phylogenies
    • Otto, W., Stadler, P.F., Lopez-Giraldez, F., Townsend, J.P., Lynch, V.J. and Wagner, G.P. (2009) Measuring transcription factor-binding site turnover: a maximum likelihood approach using phylogenies. Genome Biol. Evol., 1, 85-98.
    • (2009) Genome Biol. Evol. , vol.1 , pp. 85-98
    • Otto, W.1    Stadler, P.F.2    Lopez-Giraldez, F.3    Townsend, J.P.4    Lynch, V.J.5    Wagner, G.P.6
  • 12
    • 79955471381 scopus 로고    scopus 로고
    • High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
    • He, Q., Bardet, A.F., Patton, B., Purvis, J., Johnston, J., Paulson, A., Gogol, M., Stark, A. and Zeitlinger, J. (2011) High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat. Genet., 43, 414-420.
    • (2011) Nat. Genet. , vol.43 , pp. 414-420
    • He, Q.1    Bardet, A.F.2    Patton, B.3    Purvis, J.4    Johnston, J.5    Paulson, A.6    Gogol, M.7    Stark, A.8    Zeitlinger, J.9
  • 13
    • 36949006682 scopus 로고    scopus 로고
    • MORPH: Probabilistic alignment combined with hidden Markov models of cis-regulatory modules
    • Sinha, S. and He, X. (2007) MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules. PLoS Comput. Biol., 3, e216.
    • (2007) PLoS Comput. Biol. , vol.3
    • Sinha, S.1    He, X.2
  • 14
    • 34548763908 scopus 로고    scopus 로고
    • Incorporating evolution of transcription factor binding sites into annotated alignments
    • Special Issue - Bioinformatics: from Molecules to Systems August 2007
    • Bais, A.S., Grossmann, S. and Vingron, M. (2007) Incorporating evolution of transcription factor binding sites into annotated alignments. J. Biosci., 32, 841-850. (Pubitemid 47435516)
    • (2007) Journal of Biosciences , vol.32 , Issue.5 , pp. 841-850
    • Bais, A.S.1    Grossmann, S.2    Vingron, M.3
  • 15
    • 30344439849 scopus 로고    scopus 로고
    • Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity
    • DOI 10.1016/j.cell.2005.10.042, PII S0092867405013954
    • Hallikas, O., Palin, K., Sinjushina, N., Rautiainen, R., Partanen, J., Ukkonen, E. and Taipale, J. (2006) Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell, 124, 47-59. (Pubitemid 43069309)
    • (2006) Cell , vol.124 , Issue.1 , pp. 47-59
    • Hallikas, O.1    Palin, K.2    Sinjushina, N.3    Rautiainen, R.4    Partanen, J.5    Ukkonen, E.6    Taipale, J.7
  • 16
    • 78651255620 scopus 로고    scopus 로고
    • Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs
    • Majoros, W.H. and Ohler, U. (2010) Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs. PLoS Comput. Biol., 6, e1001037.
    • (2010) PLoS Comput. Biol. , vol.6
    • Majoros, W.H.1    Ohler, U.2
  • 17
    • 79952116707 scopus 로고    scopus 로고
    • Dinucleotide weight matrices for predicting transcription factor binding sites: Generalizing the position weight matrix
    • Siddharthan, R. (2010) Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix. PLoS One, 5, e9722.
    • (2010) PLoS One , vol.5
    • Siddharthan, R.1
  • 19
    • 59649095778 scopus 로고    scopus 로고
    • Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues
    • Lu, Y. and Sze, S.H. (2009) Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues. Nucleic Acids Res., 37, 463-472.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 463-472
    • Lu, Y.1    Sze, S.H.2
  • 21
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for fast and accurate multiple sequence alignment
    • Notredame, C., Higgins, D.G. and Heringa, J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
    • (2000) J. Mol. Biol. , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 22
    • 76949098763 scopus 로고    scopus 로고
    • Towards realistic benchmarks for multiple alignments of non-coding sequences
    • Kim, J. and Sinha, S. (2010) Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics, 11, 54.
    • (2010) BMC Bioinformatics , vol.11 , pp. 54
    • Kim, J.1    Sinha, S.2
  • 23
    • 42949147755 scopus 로고    scopus 로고
    • Phylogenetic simulation of promoter evolution: Estimation and modeling of binding site turnover events and assessment of their impact on alignment tools
    • Huang, W., Nevins, J.R. and Ohler, U. (2007) Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools. Genome Biol., 8, R225.
    • (2007) Genome Biol. , vol.8
    • Huang, W.1    Nevins, J.R.2    Ohler, U.3
  • 25
    • 1542316915 scopus 로고    scopus 로고
    • MCALIGN: Stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution
    • DOI 10.1101/gr.1571904
    • Keightley, P.D. and Johnson, T. (2004) MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution. Genome Res., 14, 442-450. (Pubitemid 38380398)
    • (2004) Genome Research , vol.14 , Issue.3 , pp. 442-450
    • Keightley, P.D.1    Johnson, T.2
  • 28
    • 14644430471 scopus 로고    scopus 로고
    • ProbCons: Probabilistic consistency-based multiple sequence alignment
    • DOI 10.1101/gr.2821705
    • Do, C.B., Mahabhashyam, M.S., Brudno, M. and Batzoglou, S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340. (Pubitemid 40309398)
    • (2005) Genome Research , vol.15 , Issue.2 , pp. 330-340
    • Do, C.B.1    Mahabhashyam, M.S.P.2    Brudno, M.3    Batzoglou, S.4
  • 29
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 30
    • 45949107473 scopus 로고    scopus 로고
    • Recent developments in the MAFFT multiple sequence alignment program
    • DOI 10.1093/bib/bbn013, Special Issue: Critical Technologies for Bioinformatics
    • Katoh, K. and Toh, H. (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief. Bioinform., 9, 286-298. (Pubitemid 351890825)
    • (2008) Briefings in Bioinformatics , vol.9 , Issue.4 , pp. 286-298
    • Katoh, K.1    Toh, H.2
  • 31
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci., 89, 10915-10919.
    • (1992) Proc. Natl Acad. Sci. , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 32
    • 83255194564 scopus 로고    scopus 로고
    • Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data
    • Althammer, S., Gonzalez-Vallinas, J., Ballare, C., Beato, M. and Eyras, E. (2011) Pyicos: A versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics, 27, 3333-3340.
    • (2011) Bioinformatics , vol.27 , pp. 3333-3340
    • Althammer, S.1    Gonzalez-Vallinas, J.2    Ballare, C.3    Beato, M.4    Eyras, E.5
  • 35
    • 65249089637 scopus 로고    scopus 로고
    • Local DNA topography correlates with functional noncoding regions of the human genome
    • Parker, S.C., Hansen, L., Abaan, H.O., Tullius, T.D. and Margulies, E.H. (2009) Local DNA topography correlates with functional noncoding regions of the human genome. Science, 324, 389-392.
    • (2009) Science , vol.324 , pp. 389-392
    • Parker, S.C.1    Hansen, L.2    Abaan, H.O.3    Tullius, T.D.4    Margulies, E.H.5
  • 36
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • Bulyk, M.L., Johnson, P.L. and Church, G.M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res., 30, 1255-1261. (Pubitemid 34679700)
    • (2002) Nucleic Acids Research , vol.30 , Issue.5 , pp. 1255-1261
    • Bulyk, M.L.1    Johnson, P.L.F.2    Church, G.M.3
  • 38
    • 78649828754 scopus 로고    scopus 로고
    • Issues in bioinformatics benchmarking: The case study of multiple sequence alignment
    • Aniba, M.R., Poch, O. and Thompson, J.D. Issues in bioinformatics benchmarking: the case study of multiple sequence alignment. Nucleic Acids Res., 38, 7353-7363.
    • Nucleic Acids Res. , vol.38 , pp. 7353-7363
    • Aniba, M.R.1    Poch, O.2    Thompson, J.D.3
  • 39
    • 59149102602 scopus 로고    scopus 로고
    • Phylogenetic and functional assessment of orthologs inference projects and methods
    • Altenhoff, A.M. and Dessimoz, C. (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput. Biol., 5, e1000262.
    • (2009) PLoS Comput. Biol. , vol.5
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 40
    • 33846869288 scopus 로고    scopus 로고
    • Multiple sequence alignment: In pursuit of homologous DNA positions
    • DOI 10.1101/gr.5232407
    • Kumar, S. and Filipski, A. (2007) Multiple sequence alignment: in pursuit of homologous DNA positions. Genome Res., 17, 127-135. (Pubitemid 46220757)
    • (2007) Genome Research , vol.17 , Issue.2 , pp. 127-135
    • Kumar, S.1    Filipski, A.2
  • 41
    • 70349866695 scopus 로고    scopus 로고
    • Upcoming challenges for multiple sequence alignment methods in the high-throughput era
    • Kemena, C. and Notredame, C. (2009) Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 25, 2455-2465.
    • (2009) Bioinformatics , vol.25 , pp. 2455-2465
    • Kemena, C.1    Notredame, C.2
  • 42
    • 79953307693 scopus 로고    scopus 로고
    • A comprehensive benchmark study of multiple sequence alignment methods: Current challenges and future perspectives
    • Thompson, J.D., Linard, B., Lecompte, O. and Poch, O. (2011) A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One, 6, e18093.
    • (2011) PLoS One , vol.6
    • Thompson, J.D.1    Linard, B.2    Lecompte, O.3    Poch, O.4
  • 43
    • 35748929942 scopus 로고    scopus 로고
    • DNA reference alignment benchmarks based on tertiary structure of encoded proteins
    • DOI 10.1093/bioinformatics/btm389
    • Carroll, H., Beckstead, W., O'Connor, T., Ebbert, M., Clement, M., Snell, Q. and McClellan, D. (2007) DNA reference alignment benchmarks based on tertiary structure of encoded proteins. Bioinformatics, 23, 2648-2649. (Pubitemid 350048377)
    • (2007) Bioinformatics , vol.23 , Issue.19 , pp. 2648-2649
    • Carroll, H.1    Beckstead, W.2    O'Connor, T.3    Ebbert, M.4    Clement, M.5    Snell, Q.6    Mcclellan, D.7
  • 44
    • 33750218960 scopus 로고    scopus 로고
    • PhyloGibbs: A Gibbs sampling motif finder that incorporates phylogeny
    • Siddharthan, R., Siggia, E.D. and 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
  • 45
    • 22144491990 scopus 로고    scopus 로고
    • MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
    • Moses, A.M., Chiang, D.Y., Pollard, D.A., Iyer, V.N. and Eisen, M.B. (2004) MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol., 5, R98.
    • (2004) Genome Biol. , vol.5
    • Moses, A.M.1    Chiang, D.Y.2    Pollard, D.A.3    Iyer, V.N.4    Eisen, M.B.5
  • 46
    • 84857180279 scopus 로고    scopus 로고
    • MotEvo: Integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences
    • doi:10.1093/bioinformatics/btr695 [epub ahead of print]
    • Arnold, P., Erb, I., Pachkov, M., Molina, N. and van Nimwegen, E. MotEvo: Integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics, doi:10.1093/bioinformatics/btr695 [epub ahead of print].
    • Bioinformatics
    • Arnold, P.1    Erb, I.2    Pachkov, M.3    Molina, N.4    Van Nimwegen, E.5
  • 47
    • 78651230601 scopus 로고    scopus 로고
    • Assessing computational methods of cis-regulatory module prediction
    • Su, J., Teichmann, S.A. and Down, T.A. Assessing computational methods of cis-regulatory module prediction. PLoS Comput. Biol., 6, e1001020.
    • PLoS Comput. Biol. , vol.6
    • Su, J.1    Teichmann, S.A.2    Down, T.A.3


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