메뉴 건너뛰기




Volumn 14, Issue , 2013, Pages

LASAGNA: A novel algorithm for transcription factor binding site alignment

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT ALGORITHMS; ALIGNMENT-FREE; CHROMATIN IMMUNOPRECIPITATION; NOVEL ALGORITHM; POSITION DEPENDENCE; PUBLIC DATABASE; SCORING MATRICES; TRANSCRIPTION FACTOR BINDING SITES;

EID: 84875170740     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-108     Document Type: Article
Times cited : (23)

References (53)
  • 7
    • 27644521314 scopus 로고    scopus 로고
    • Exact algorithms for planted motif problems
    • 10.1089/cmb.2005.12.1117, 16241901
    • Rajasekaran S, Balla S, Huang CH. Exact algorithms for planted motif problems. J Comput Biol 2005, 12(8):1117-1128. 10.1089/cmb.2005.12.1117, 16241901.
    • (2005) J Comput Biol , vol.12 , Issue.8 , pp. 1117-1128
    • Rajasekaran, S.1    Balla, S.2    Huang, C.H.3
  • 9
    • 33747044757 scopus 로고    scopus 로고
    • Analysis of computational approaches for motif discovery
    • 10.1186/1748-7188-1-8, 1540429, 16722558
    • Li N, Tompa M. Analysis of computational approaches for motif discovery. Algorithms Mol Biol 2006, 1:8. 10.1186/1748-7188-1-8, 1540429, 16722558.
    • (2006) Algorithms Mol Biol , vol.1 , pp. 8
    • Li, N.1    Tompa, M.2
  • 10
    • 34248380020 scopus 로고    scopus 로고
    • A combinatorial optimization approach for diverse motif finding applications
    • 10.1186/1748-7188-1-13, 1570465, 16916460
    • Zaslavsky E, Singh M. A combinatorial optimization approach for diverse motif finding applications. Algorithms Mol Biol 2006, 1:13. 10.1186/1748-7188-1-13, 1570465, 16916460.
    • (2006) Algorithms Mol Biol , vol.1 , pp. 13
    • Zaslavsky, E.1    Singh, M.2
  • 11
    • 63549134757 scopus 로고    scopus 로고
    • M are better than one: an ensemble-based motif finder and its application to regulatory element prediction
    • 10.1093/bioinformatics/btp090, 2660878, 19223448
    • Yanover C, Singh M, Zaslavsky E. M are better than one: an ensemble-based motif finder and its application to regulatory element prediction. Bioinformatics 2009, 25(7):868-874. 10.1093/bioinformatics/btp090, 2660878, 19223448.
    • (2009) Bioinformatics , vol.25 , Issue.7 , pp. 868-874
    • Yanover, C.1    Singh, M.2    Zaslavsky, E.3
  • 12
    • 77949476121 scopus 로고    scopus 로고
    • Evidence-ranked motif identification
    • 10.1186/gb-2010-11-2-r19, 2872879, 20156354
    • Georgiev S, Boyle A, Jayasurya K, Ding X, Mukherjee S, Ohler U. Evidence-ranked motif identification. Genome Biol 2010, 11(2):R19. 10.1186/gb-2010-11-2-r19, 2872879, 20156354.
    • (2010) Genome Biol , vol.11 , Issue.2
    • Georgiev, S.1    Boyle, A.2    Jayasurya, K.3    Ding, X.4    Mukherjee, S.5    Ohler, U.6
  • 13
    • 12344291347 scopus 로고    scopus 로고
    • Comparative analysis of methods for representing and searching for transcription factor binding sites
    • 10.1093/bioinformatics/bth438, 15297295
    • Osada R, Zaslavsky E, Singh M. Comparative analysis of methods for representing and searching for transcription factor binding sites. Bioinformatics 2004, 20(18):3516-3525. 10.1093/bioinformatics/bth438, 15297295.
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3516-3525
    • Osada, R.1    Zaslavsky, E.2    Singh, M.3
  • 14
    • 23144431724 scopus 로고    scopus 로고
    • P-Match: transcription factor binding site search by combining patterns and weight matrices
    • 1160202, 15980505
    • Chekmenev DS, Haid C, Kel AE. P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res 2005, 33(suppl 2):W432-W437. 1160202, 15980505.
    • (2005) Nucleic Acids Res , vol.33 , Issue.SUPPL. 2
    • Chekmenev, D.S.1    Haid, C.2    Kel, A.E.3
  • 15
    • 44349109637 scopus 로고    scopus 로고
    • Eukaryotic transcription factor binding sites-modeling and integrative search methods.
    • 10.1093/bioinformatics/btn198, 18426806
    • Hannenhalli S. Eukaryotic transcription factor binding sites-modeling and integrative search methods. Bioinformatics 2008, 24(11):1325-1331. 10.1093/bioinformatics/btn198, 18426806.
    • (2008) Bioinformatics , vol.24 , Issue.11 , pp. 1325-1331
    • Hannenhalli, S.1
  • 16
    • 77955869106 scopus 로고    scopus 로고
    • Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction
    • 10.1093/nar/gkq274, 2896541, 20439311
    • Salama RA, Stekel DJ. Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction. Nucleic Acids Res 2010, 38(12):e135. 10.1093/nar/gkq274, 2896541, 20439311.
    • (2010) Nucleic Acids Res , vol.38 , Issue.12
    • Salama, R.A.1    Stekel, D.J.2
  • 17
    • 80053946203 scopus 로고    scopus 로고
    • SiTaR: a novel tool for transcription factor binding site prediction
    • 10.1093/bioinformatics/btr492, 21893518
    • Fazius E, Shelest V, Shelest E. SiTaR: a novel tool for transcription factor binding site prediction. Bioinformatics 2011, 27:2806-2811. 10.1093/bioinformatics/btr492, 21893518.
    • (2011) Bioinformatics , vol.27 , pp. 2806-2811
    • Fazius, E.1    Shelest, V.2    Shelest, E.3
  • 18
    • 0021760026 scopus 로고
    • Computer methods to locate signals in nucleic acid sequences
    • 10.1093/nar/12.1Part2.505, 321067, 6364039
    • Staden R. Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res 1984, 12(1Part2):505-519. 10.1093/nar/12.1Part2.505, 321067, 6364039.
    • (1984) Nucleic Acids Res , vol.12 , Issue.1 PART 2 , pp. 505-519
    • Staden, R.1
  • 19
    • 26444442910 scopus 로고    scopus 로고
    • Using TESS to predict transcription factor binding sites in DNA sequence
    • J Wiley and Sons, Baxevanis AD, Baxevanis AD
    • Schug J. Using TESS to predict transcription factor binding sites in DNA sequence. Current Protocols in Bioinformatics 2003, J Wiley and Sons, Baxevanis AD, Baxevanis AD.
    • (2003) Current Protocols in Bioinformatics
    • Schug, J.1
  • 20
    • 0041853625 scopus 로고    scopus 로고
    • MATCH™: a tool for searching transcription factor binding sites in DNA sequences
    • 10.1093/nar/gkg585, 169193, 12824369
    • Kel A, Gößling E, Reuter I, Cheremushkin E, Kel-Margoulis O, Wingender E. MATCH™: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003, 31(13):3576-3579. 10.1093/nar/gkg585, 169193, 12824369.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3576-3579
    • Kel, A.1    Gößling, E.2    Reuter, I.3    Cheremushkin, E.4    Kel-Margoulis, O.5    Wingender, E.6
  • 21
    • 3242891274 scopus 로고    scopus 로고
    • ConSite: web-based prediction of regulatory elements using cross-species comparison
    • 441510, 15215389
    • Sandelin A, Wasserman WW, Lenhard B. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 2004, 32(suppl 2):W249-W252. 441510, 15215389.
    • (2004) Nucleic Acids Res , vol.32 , Issue.SUPPL. 2
    • Sandelin, A.1    Wasserman, W.W.2    Lenhard, B.3
  • 22
    • 52749097035 scopus 로고    scopus 로고
    • Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
    • 10.1038/nprot.2008.97, 18802439
    • Turatsinze JVV, Thomas-Chollier M, Defrance M, van H. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc 2008, 3(10):1578-1588. 10.1038/nprot.2008.97, 18802439.
    • (2008) Nat Protoc , vol.3 , Issue.10 , pp. 1578-1588
    • Turatsinze, J.V.V.1    Thomas-Chollier, M.2    Defrance, M.3    van, H.4
  • 23
    • 67849114236 scopus 로고    scopus 로고
    • Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
    • 2703934, 19487240
    • Zambelli F, Pesole G, Pavesi G. Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Res 2009, 37(suppl 2):W247-W252. 2703934, 19487240.
    • (2009) Nucleic Acids Res , vol.37 , Issue.SUPPL. 2
    • Zambelli, F.1    Pesole, G.2    Pavesi, G.3
  • 24
    • 77954288773 scopus 로고    scopus 로고
    • TransFind-predicting transcriptional regulators for gene sets
    • 2896106, 20511592
    • Kiełbasa SM, Klein H, Roider HG, Vingron M, Blüthgen N. TransFind-predicting transcriptional regulators for gene sets. Nucleic Acids Res 2010, 38(suppl 2):W275-W280. 2896106, 20511592.
    • (2010) Nucleic Acids Res , vol.38 , Issue.SUPPL. 2
    • Kiełbasa, S.M.1    Klein, H.2    Roider, H.G.3    Vingron, M.4    Blüthgen, N.5
  • 30
    • 77954188309 scopus 로고    scopus 로고
    • Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution
    • 2881384, 20529918
    • Kumar A, Cowen L. Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution. Bioinformatics 2010, 26(12):i287-i293. 2881384, 20529918.
    • (2010) Bioinformatics , vol.26 , Issue.12
    • Kumar, A.1    Cowen, L.2
  • 31
    • 0027968068 scopus 로고
    • 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(22):4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
    • (1994) Nucleic Acids Res , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3    Clustal, W.4
  • 33
    • 13444270902 scopus 로고    scopus 로고
    • The MAPPER database: a multi-genome catalog of putative transcription factor binding sites
    • 1160266, 15980506
    • Marinescu VD, Kohane IS, Riva A. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res 2005, 33(suppl 1):D91-D97. 1160266, 15980506.
    • (2005) Nucleic Acids Res , vol.33 , Issue.SUPPL. 1
    • Marinescu, V.D.1    Kohane, I.S.2    Riva, A.3
  • 34
    • 34548400364 scopus 로고    scopus 로고
    • Recent evolutions of multiple sequence alignment algorithms
    • 10.1371/journal.pcbi.0030123, 1963500, 17784778
    • Notredame C. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol 2007, 3(8):e123. 10.1371/journal.pcbi.0030123, 1963500, 17784778.
    • (2007) PLoS Comput Biol , vol.3 , Issue.8
    • Notredame, C.1
  • 36
    • 58149179991 scopus 로고    scopus 로고
    • The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences
    • 2686574, 18971253
    • Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW. The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic Acids Res 2009, 37(suppl 1):D54-D60. 2686574, 18971253.
    • (2009) Nucleic Acids Res , vol.37 , Issue.SUPPL. 1
    • Portales-Casamar, E.1    Arenillas, D.2    Lim, J.3    Swanson, M.I.4    Jiang, S.5    McCallum, A.6    Kirov, S.7    Wasserman, W.W.8
  • 37
    • 0023042012 scopus 로고
    • Information content of binding sites on nucleotide sequences
    • 10.1016/0022-2836(86)90165-8, 3525846
    • Schneider TD, Stormo GD, Gold L, Ehrenfeucht A. Information content of binding sites on nucleotide sequences. J Mol Biol 1986, 188(3):415-431. 10.1016/0022-2836(86)90165-8, 3525846.
    • (1986) J Mol Biol , vol.188 , Issue.3 , pp. 415-431
    • Schneider, T.D.1    Stormo, G.D.2    Gold, L.3    Ehrenfeucht, A.4
  • 38
    • 34250159524 scopus 로고    scopus 로고
    • Genome-Wide Mapping of in Vivo Protein-DNA Interactions
    • 10.1126/science.1141319, 17540862
    • Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-Wide Mapping of in Vivo Protein-DNA Interactions. Science 2007, 316(5830):1497-1502. 10.1126/science.1141319, 17540862.
    • (2007) Science , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 40
    • 0032861774 scopus 로고    scopus 로고
    • SCPD: a promoter database of the yeast Saccharomyces cerevisiae
    • 10.1093/bioinformatics/15.7.607, 10487868
    • Zhu J, Zhang MQ. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 1999, 15(7):607-611. 10.1093/bioinformatics/15.7.607, 10487868.
    • (1999) Bioinformatics , vol.15 , Issue.7 , pp. 607-611
    • Zhu, J.1    Zhang, M.Q.2
  • 41
    • 0036084691 scopus 로고    scopus 로고
    • EuGenes: a eukaryote genome information system
    • 10.1093/nar/30.1.145, 99146, 11752277
    • Gilbert DG. euGenes: a eukaryote genome information system. Nucleic Acids Res 2002, 30:145-148. 10.1093/nar/30.1.145, 99146, 11752277.
    • (2002) Nucleic Acids Res , vol.30 , pp. 145-148
    • Gilbert, D.G.1
  • 42
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett T. An introduction to ROC analysis. Pattern Recogn Lett 2006, 27:861-874.
    • (2006) Pattern Recogn Lett , vol.27 , pp. 861-874
    • Fawcett, T.1
  • 43
    • 0001884644 scopus 로고
    • Individual comparisons by ranking methods
    • Wilcoxon F. Individual comparisons by ranking methods. Biometrics Bull 1945, 1(6):80-83.
    • (1945) Biometrics Bull , vol.1 , Issue.6 , pp. 80-83
    • Wilcoxon, F.1
  • 44
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • 10.1038/nature11247, 3439153, 22955616, Consortium TEP
    • Consortium TEP An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. 10.1038/nature11247, 3439153, 22955616, Consortium TEP.
    • (2012) Nature , vol.489 , pp. 57-74
  • 45
    • 84857859359 scopus 로고    scopus 로고
    • RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
    • 10.1093/nar/gkr1104, 3287167, 22156162
    • Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van H. RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 2012, 40(4):e31. 10.1093/nar/gkr1104, 3287167, 22156162.
    • (2012) Nucleic Acids Res , vol.40 , Issue.4
    • Thomas-Chollier, M.1    Herrmann, C.2    Defrance, M.3    Sand, O.4    Thieffry, D.5    van, H.6
  • 46
    • 68949213578 scopus 로고    scopus 로고
    • Insights from genomic profiling of transcription factors
    • 10.1038/nrg2636, 2846386, 19668247
    • Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10(9):605-616. 10.1038/nrg2636, 2846386, 19668247.
    • (2009) Nat Rev Genet , vol.10 , Issue.9 , pp. 605-616
    • Farnham, P.J.1
  • 47
    • 34447506667 scopus 로고    scopus 로고
    • Quantifying similarity between motifs
    • 10.1186/gb-2007-8-2-r24, 1852410, 17324271
    • Gupta S, Stamatoyannopoulos J, Bailey T, Noble W. Quantifying similarity between motifs. Genome Biol 2007, 8(2):R24. 10.1186/gb-2007-8-2-r24, 1852410, 17324271.
    • (2007) Genome Biol , vol.8 , Issue.2
    • Gupta, S.1    Stamatoyannopoulos, J.2    Bailey, T.3    Noble, W.4
  • 48
    • 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 Res 2004, 14(6):1188-1190. 10.1101/gr.849004, 419797, 15173120.
    • (2004) Genome Res , vol.14 , Issue.6 , pp. 1188-1190
    • Crooks, G.E.1    Hon, G.2    Chandonia, J.M.3    Brenner, S.E.4
  • 49
    • 82755162143 scopus 로고    scopus 로고
    • C-Myb and GATA-3 cooperatively regulate IL-13 expression via conserved GATA-3 response element and recruit mixed lineage leukemia (MLL) for histone modification of the IL-13 Locus
    • 10.4049/jimmunol.1100550, 3221810, 22039304
    • Kozuka T, Sugita M, Shetzline S, Gewirtz AM, Nakata Y. c-Myb and GATA-3 cooperatively regulate IL-13 expression via conserved GATA-3 response element and recruit mixed lineage leukemia (MLL) for histone modification of the IL-13 Locus. J Immunol 2011, 187(11):5974-5982. 10.4049/jimmunol.1100550, 3221810, 22039304.
    • (2011) J Immunol , vol.187 , Issue.11 , pp. 5974-5982
    • Kozuka, T.1    Sugita, M.2    Shetzline, S.3    Gewirtz, A.M.4    Nakata, Y.5
  • 50
    • 0033617297 scopus 로고    scopus 로고
    • Regulation of the human Interleukin-5 promoter by Ets Transcription Factors: ETS1 AND ETS2, BUT NOT ELF-1, COOPERATE WITH GATA3 AND HTLV-I TAX1
    • 10.1074/jbc.274.18.12910, 10212281
    • Blumenthal SG, Aichele G, Wirth T, Czernilofsky AP, Nordheim A, Dittmer J. Regulation of the human Interleukin-5 promoter by Ets Transcription Factors: ETS1 AND ETS2, BUT NOT ELF-1, COOPERATE WITH GATA3 AND HTLV-I TAX1. J Biol Chem 1999, 274(18):12910-12916. 10.1074/jbc.274.18.12910, 10212281.
    • (1999) J Biol Chem , vol.274 , Issue.18 , pp. 12910-12916
    • Blumenthal, S.G.1    Aichele, G.2    Wirth, T.3    Czernilofsky, A.P.4    Nordheim, A.5    Dittmer, J.6
  • 51
    • 31544470129 scopus 로고    scopus 로고
    • A role for Ets1, synergizing with AP-1 and GATA-3 in the regulation of IL-5 transcription in mouse Th2 lymphocytes
    • Wang J, Shannon MF, Young IG. A role for Ets1, synergizing with AP-1 and GATA-3 in the regulation of IL-5 transcription in mouse Th2 lymphocytes. Int Immunol 2006, 18(2):313-323.
    • (2006) Int Immunol , vol.18 , Issue.2 , pp. 313-323
    • Wang, J.1    Shannon, M.F.2    Young, I.G.3
  • 52
    • 39749102250 scopus 로고    scopus 로고
    • A comparative study on computational two-block motif detection: algorithms and applications
    • Bi C, Leeder J, Vyhlidal C. A comparative study on computational two-block motif detection: algorithms and applications. Mol Pharm 2007, 5:3-16.
    • (2007) Mol Pharm , vol.5 , pp. 3-16
    • Bi, C.1    Leeder, J.2    Vyhlidal, C.3
  • 53
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • 10.1093/bioinformatics/15.7.563, 10487864
    • Hertz GZ, Stormo GD. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15(7):563-577. 10.1093/bioinformatics/15.7.563, 10487864.
    • (1999) Bioinformatics , vol.15 , Issue.7 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.