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Volumn 13, Issue 1, 2012, Pages

Towards a theoretical understanding of false positives in DNA motif finding

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM DEVELOPMENT; BENCHMARK STUDY; COMPUTATIONAL BIOLOGY; DATA SET SIZE; DNA MOTIF; FALSE POSITIVE; GIBBS SAMPLERS; MOTIF FINDING; SEARCH SPACES; SEQUENCE LENGTHS; THEORETICAL PREDICTION;

EID: 84862751090     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-151     Document Type: Article
Times cited : (21)

References (48)
  • 1
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • 10.1038/nrg1315, 15131651
    • Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5:276-287. 10.1038/nrg1315, 15131651.
    • (2004) Nat Rev Genet , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 2
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif finding algorithms
    • Das MK, Dai HK. A survey of DNA motif finding algorithms. BMC Bioinforma 2007, 8(Suppl. 7):S21.
    • (2007) BMC Bioinforma , vol.8 , Issue.SUPPL. 7
    • Das, M.K.1    Dai, H.K.2
  • 3
    • 80051584659 scopus 로고    scopus 로고
    • Regulatory Motif Analysis
    • Springer Science + Business Media LLC, , Edwards D
    • Moses AM, Sinha S, et al. Regulatory Motif Analysis. Bioinformatics: Tools and Applications 2009, 137-163. Springer Science + Business Media LLC, , Edwards D.
    • (2009) Bioinformatics: Tools and Applications , pp. 137-163
    • Moses, A.M.1    Sinha, S.2
  • 6
    • 26444584579 scopus 로고    scopus 로고
    • Limitations and potentials of current motif discovery algorithms
    • 10.1093/nar/gki791, 1199555, 16284194
    • Hu J, Li B, Kihara D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res 2005, 33(15):4899-4913. 10.1093/nar/gki791, 1199555, 16284194.
    • (2005) Nucleic Acids Res , vol.33 , Issue.15 , pp. 4899-4913
    • Hu, J.1    Li, B.2    Kihara, D.3
  • 7
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • 10.1038/84792, 11175784
    • Bussemaker H, Li H, Siggia E. Regulatory element detection using correlation with expression. Nat Genet 2001, 27(2):167-171. 10.1038/84792, 11175784.
    • (2001) Nat Genet , vol.27 , Issue.2 , pp. 167-171
    • Bussemaker, H.1    Li, H.2    Siggia, E.3
  • 8
    • 33746691336 scopus 로고    scopus 로고
    • Extensive low-affinity transcriptional interactions in the yeast genome
    • 10.1101/gr.5113606, 1524868, 16809671
    • Tanay A. Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 2006, 16(8):962-972. 10.1101/gr.5113606, 1524868, 16809671.
    • (2006) Genome Res , vol.16 , Issue.8 , pp. 962-972
    • Tanay, A.1
  • 9
    • 33748191291 scopus 로고    scopus 로고
    • Statistical mechanical modelling of genome-wide transcription factor occupancy data by matrix reduce
    • 10.1093/bioinformatics/btl223, 16873464
    • Foat BC, Morozov AV, Bussemaker HJ. Statistical mechanical modelling of genome-wide transcription factor occupancy data by matrix reduce. Bioinformatics 2006, 22(14):e141-e149. 10.1093/bioinformatics/btl223, 16873464.
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Foat, B.C.1    Morozov, A.V.2    Bussemaker, H.J.3
  • 10
    • 34047230770 scopus 로고    scopus 로고
    • Discovering motifs in ranked lists of DNA sequences
    • 10.1371/journal.pcbi.0030039, 1829477, 17381235
    • Eden E, Lipson D, Yogev S, Yakhini Z. Discovering motifs in ranked lists of DNA sequences. PLoS Comput Biol 2007, 3(3):e39. 10.1371/journal.pcbi.0030039, 1829477, 17381235.
    • (2007) PLoS Comput Biol , vol.3 , Issue.3
    • Eden, E.1    Lipson, D.2    Yogev, S.3    Yakhini, Z.4
  • 11
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 10.1038/nature01644, 12748633
    • Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423(6937):241-254. 10.1038/nature01644, 12748633.
    • (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
  • 12
    • 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(18):2369-2380. 10.1093/bioinformatics/btg329, 14668220.
    • (2003) Bioinformatics , vol.19 , Issue.18 , pp. 2369-2380
    • Wang, T.1    Stormo, G.D.2
  • 13
    • 33750218960 scopus 로고    scopus 로고
    • PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny
    • Siddharthan S, Siggia ED, Nimwegen EV. PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Computat Biol 2005, 1(7):e67.
    • (2005) PLoS Computat Biol , vol.1 , Issue.7
    • Siddharthan, S.1    Siggia, E.D.2    Nimwegen, E.V.3
  • 16
    • 34249862425 scopus 로고    scopus 로고
    • Connecting protein structure with predictions of regulatory sites
    • 10.1073/pnas.0701356104, 1855371, 17438293
    • Morozov AV, Siggia ED. Connecting protein structure with predictions of regulatory sites. Proc Nat Acad Sci USA 2007, 104(17):7068-7073. 10.1073/pnas.0701356104, 1855371, 17438293.
    • (2007) Proc Nat Acad Sci USA , vol.104 , Issue.17 , pp. 7068-7073
    • Morozov, A.V.1    Siggia, E.D.2
  • 17
    • 34547418057 scopus 로고    scopus 로고
    • Nucleotide occupancy information improves de novo motif discovery
    • Narlikar L, Gordan R, Hartemink AJ. Nucleotide occupancy information improves de novo motif discovery. Proceedings of RECOMB 2007, 107-121.
    • (2007) Proceedings of RECOMB , pp. 107-121
    • Narlikar, L.1    Gordan, R.2    Hartemink, A.J.3
  • 18
    • 67651229820 scopus 로고    scopus 로고
    • Factoring local sequence composition in motif significance analysis
    • Ng P, Keich U. Factoring local sequence composition in motif significance analysis. Genome informatics 2008, 21:15-26.
    • (2008) Genome informatics , vol.21 , pp. 15-26
    • Ng, P.1    Keich, U.2
  • 19
    • 4544295425 scopus 로고    scopus 로고
    • Environmentally induced foregut remodelling by PHA-4/FoxA and DAF-12/NHR
    • 10.1126/science.1102216, 15375261
    • Ao W, Gaudet J, Kent WJ, Muttumu S, Mango SE. Environmentally induced foregut remodelling by PHA-4/FoxA and DAF-12/NHR. Science 2004, 305:1743-1746. 10.1126/science.1102216, 15375261.
    • (2004) Science , vol.305 , pp. 1743-1746
    • Ao, W.1    Gaudet, J.2    Kent, W.J.3    Muttumu, S.4    Mango, S.E.5
  • 20
    • 28444456845 scopus 로고    scopus 로고
    • Rare events and conditional events on random strings
    • Régnier M, Denise A. Rare events and conditional events on random strings. Discrete Math Theor Comput Sci 2004, 6:191-214.
    • (2004) Discrete Math Theor Comput Sci , vol.6 , pp. 191-214
    • Régnier, M.1    Denise, A.2
  • 22
    • 0036772507 scopus 로고    scopus 로고
    • Subtle motifs: defining the limits of motif finding algorithms
    • 10.1093/bioinformatics/18.10.1382, 12376383
    • Keich U, Pevzner PA. Subtle motifs: defining the limits of motif finding algorithms. Bioinformatics 2002, 18(10):1382-1390. 10.1093/bioinformatics/18.10.1382, 12376383.
    • (2002) Bioinformatics , vol.18 , Issue.10 , pp. 1382-1390
    • Keich, U.1    Pevzner, P.A.2
  • 23
    • 0024604438 scopus 로고
    • Methods for calculating the probabilities of finding patterns in sequences
    • Staden R. Methods for calculating the probabilities of finding patterns in sequences. Computat Appl Biosci 1989, 5(2):89-96.
    • (1989) Computat Appl Biosci , vol.5 , Issue.2 , pp. 89-96
    • Staden, R.1
  • 24
    • 34047159557 scopus 로고    scopus 로고
    • Computing exact p-values for DNA motifs
    • 10.1093/bioinformatics/btl662, 17237046
    • Zhang J, Jiang B, Li M, Tromp J, Zhang X, Zhang MQ. Computing exact p-values for DNA motifs. Bioinformatics 2007, 23(5):531-537. 10.1093/bioinformatics/btl662, 17237046.
    • (2007) Bioinformatics , vol.23 , Issue.5 , pp. 531-537
    • Zhang, J.1    Jiang, B.2    Li, M.3    Tromp, J.4    Zhang, X.5    Zhang, M.Q.6
  • 25
    • 28444479592 scopus 로고    scopus 로고
    • Computing the P-value of the information content from an alignment of multiple sequences
    • Nagarajan N, Jones N, Keich U. Computing the P-value of the information content from an alignment of multiple sequences. Bioinformatics 2005, 21(Supplement):i311-i318.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL.
    • Nagarajan, N.1    Jones, N.2    Keich, U.3
  • 26
    • 39149112830 scopus 로고    scopus 로고
    • FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments
    • 10.1093/bioinformatics/btm594, 18180239
    • Nagarajan N, Keich U. FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments. Bioinformatics 2008, 24(4):577-578. 10.1093/bioinformatics/btm594, 18180239.
    • (2008) Bioinformatics , vol.24 , Issue.4 , pp. 577-578
    • Nagarajan, N.1    Keich, U.2
  • 27
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz GZ, Stormo GD. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15(7-8):563-577.
    • (1999) Bioinformatics , vol.15 , Issue.7-8 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 28
    • 33748194735 scopus 로고    scopus 로고
    • Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone
    • 10.1093/bioinformatics/btl245, 16873498
    • Ng P, Nagarajan N, Jones N, Keich U. Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone. Bioinformatics 2006, 22(14):e393-e401. 10.1093/bioinformatics/btl245, 16873498.
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Ng, P.1    Nagarajan, N.2    Jones, N.3    Keich, U.4
  • 29
    • 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(1):189-200. 10.1093/nar/gkh169, 373279, 14704356.
    • (2004) Nucleic Acids Res , vol.32 , Issue.1 , pp. 189-200
    • Frith, M.C.1    Hansen, U.2    Spouge, J.L.3    Weng, Z.4
  • 30
    • 46749093391 scopus 로고    scopus 로고
    • A conservative parametric approach to motif significance analysis
    • Keich U, Ng P. A conservative parametric approach to motif significance analysis. Genome Inform 2007, 19:61-72.
    • (2007) Genome Inform , vol.19 , pp. 61-72
    • Keich, U.1    Ng, P.2
  • 32
    • 33747823564 scopus 로고    scopus 로고
    • Discovering and analyzing DNA and protein sequence motifs
    • Web Server issue
    • Bailey TL, Williams N, Misleh C, Li WW. Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34(Web Server issue):369-373.
    • (2006) Nucleic Acids Res , vol.34 , pp. 369-373
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 34
    • 52949134519 scopus 로고    scopus 로고
    • GIMSAN: a Gibbs motif finder with significant analysis
    • 10.1093/bioinformatics/btn408, 18703586
    • Ng P, Keich U. GIMSAN: a Gibbs motif finder with significant analysis. Bioinformatics 2008, 24(19):2256-2257. 10.1093/bioinformatics/btn408, 18703586.
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2256-2257
    • Ng, P.1    Keich, U.2
  • 35
    • 84874615823 scopus 로고    scopus 로고
    • GIMSAN , , http://www.cs.cornell.edu/~ppn3/gimsan.
    • GIMSAN
  • 36
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment
    • 10.1126/science.8211139, 8211139
    • Lawrence CE, Altschul SF, Boguski MS, Liu JS, Neuwald AF, Wootton JC. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 1993, 262(5131):208-214. 10.1126/science.8211139, 8211139.
    • (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
  • 37
    • 84950424966 scopus 로고
    • Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
    • Liu JS, Neuwald AF, Lawrence CE. Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J Am Stat Assoc 1995, 90(432):1156-1170.
    • (1995) J Am Stat Assoc , vol.90 , Issue.432 , pp. 1156-1170
    • Liu, J.S.1    Neuwald, A.F.2    Lawrence, C.E.3
  • 38
    • 84874626179 scopus 로고    scopus 로고
    • The Gibbs Sampler , , http://bayesweb.wadsworth.org/gibbs.
    • The Gibbs Sampler
  • 39
    • 0035224579 scopus 로고    scopus 로고
    • An algorithm for finding signals of unknown length in DNA sequences
    • Pavesi G, Mauri G, Pesole G. An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics 2001, 17(Suppl. 1):S207-S214.
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Pavesi, G.1    Mauri, G.2    Pesole, G.3
  • 40
    • 3242884167 scopus 로고    scopus 로고
    • Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    • Web Server issue
    • 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, 1(32, Web Server issue):199-203.
    • (2004) Nucleic Acids Res , vol.1 , Issue.32 , pp. 199-203
    • Pavesi, G.1    Mereghetti, P.2    Mauri, G.3    Pesole, G.4
  • 41
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: representation and discovery
    • 10.1093/bioinformatics/16.1.16, 10812473
    • Stormo GD. DNA binding sites: representation and discovery. Bioinformatics 2000, 16(1):16-23. 10.1093/bioinformatics/16.1.16, 10812473.
    • (2000) Bioinformatics , vol.16 , Issue.1 , pp. 16-23
    • Stormo, G.D.1
  • 42
    • 0031583033 scopus 로고    scopus 로고
    • Information content of individual genetic sequences
    • 10.1006/jtbi.1997.0540, 9446751
    • Schnider TD. Information content of individual genetic sequences. J Theor Biol 1997, 189(4):427-441. 10.1006/jtbi.1997.0540, 9446751.
    • (1997) J Theor Biol , vol.189 , Issue.4 , pp. 427-441
    • Schnider, T.D.1
  • 43
    • 0036137323 scopus 로고    scopus 로고
    • A higher order background model improves the detection of promoter regulatory elements by Gibbs sampling
    • 10.1093/bioinformatics/17.12.1113, 11751219
    • Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouzé P, Moreau Y. A higher order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 2001, 17(12):1113-1122. 10.1093/bioinformatics/17.12.1113, 11751219.
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1113-1122
    • Thijs, G.1    Lescot, M.2    Marchal, K.3    Rombauts, S.4    De Moor, B.5    Rouzé, P.6    Moreau, Y.7
  • 44
    • 0036108622 scopus 로고    scopus 로고
    • A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes
    • 10.1089/10665270252935566, 12015892
    • Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouzé P, Moreau Y. A Gibbs Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes. J Comput Biol 2002, 9(2):447-464. 10.1089/10665270252935566, 12015892.
    • (2002) J Comput Biol , vol.9 , Issue.2 , pp. 447-464
    • Thijs, G.1    Marchal, K.2    Lescot, M.3    Rombauts, S.4    De Moor, B.5    Rouzé, P.6    Moreau, Y.7
  • 45
    • 0033655171 scopus 로고    scopus 로고
    • ANN-SPEC: A method for discovering transcription binding sites with improved specificity
    • Workman CT, Stormo GD. ANN-SPEC: A method for discovering transcription binding sites with improved specificity. Proc Pacific Symp Biocomput 2000, 5:464-475.
    • (2000) Proc Pacific Symp Biocomput , vol.5 , pp. 464-475
    • Workman, C.T.1    Stormo, G.D.2


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