메뉴 건너뛰기




Volumn 36, Issue 21, 2008, Pages

Evolutionary computation for discovery of composite transcription factor binding sites

Author keywords

[No Author keywords available]

Indexed keywords

OCTAMER TRANSCRIPTION FACTOR 1; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 1; TRANSCRIPTION FACTOR NFAT; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN;

EID: 57149097863     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn738     Document Type: Article
Times cited : (27)

References (42)
  • 1
    • 0034714421 scopus 로고    scopus 로고
    • Gene expression data analysis
    • Brazma,A. and Vilo,J. (2000) Gene expression data analysis. FEBS Lett., 480, 17-24.
    • (2000) FEBS Lett , vol.480 , pp. 17-24
    • Brazma, A.1    Vilo, J.2
  • 2
    • 0033150947 scopus 로고    scopus 로고
    • Regulatory elements and expression profiles
    • Bucher,P. (1999) Regulatory elements and expression profiles. Curr. Opin. Struct. Biol., 9, 400-407.
    • (1999) Curr. Opin. Struct. Biol , vol.9 , pp. 400-407
    • Bucher, P.1
  • 3
    • 0032863227 scopus 로고    scopus 로고
    • Large-scale gene expression data analysis: A new challenge to computational biologist
    • Zhang,M.Q. (1999) Large-scale gene expression data analysis: A new challenge to computational biologist. Genome Res., 9, 681-688.
    • (1999) Genome Res , vol.9 , pp. 681-688
    • Zhang, M.Q.1
  • 4
    • 0035252126 scopus 로고    scopus 로고
    • Identification and analysis of eukaryotic promoters: Recent computational approaches
    • Ohler,U. and Niemann,H. (2001) Identification and analysis of eukaryotic promoters: Recent computational approaches. Trends Genet., 17 56-60.
    • (2001) Trends Genet , vol.17 , pp. 56-60
    • Ohler, U.1    Niemann, H.2
  • 5
    • 0035228215 scopus 로고    scopus 로고
    • Bioprospector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Liu,X., Brutlag,D.L. and Liu,J.S. (2001) Bioprospector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput., 6, 127-138.
    • (2001) Pac. Symp. Biocomput , vol.6 , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 6
    • 0034086773 scopus 로고    scopus 로고
    • Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
    • Jensen,L.J. and Knudsen,S. (2000) Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics, 16, 326-333.
    • (2000) Bioinformatics , vol.16 , pp. 326-333
    • Jensen, L.J.1    Knudsen, S.2
  • 7
    • 38949206269 scopus 로고    scopus 로고
    • An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach. IEEE/ACM Trans
    • Congdon,C.B., Aman,J., Nava,G., Gaskins,H.R. and Mattingly,C. (2008) An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach. IEEE/ACM Trans. Comput. Biol. Bioinf., 5 1-14.
    • (2008) Comput. Biol. Bioinf , vol.5 , pp. 1-14
    • Congdon, C.B.1    Aman, J.2    Nava, G.3    Gaskins, H.R.4    Mattingly, C.5
  • 8
    • 34547967202 scopus 로고    scopus 로고
    • Regulatory motif discovery using a population clustering evolutionary algorithm. IEEE/ACM Trans
    • Lones,M.A. and Tyrell,A.M. (2007) Regulatory motif discovery using a population clustering evolutionary algorithm. IEEE/ACM Trans. Comput. Biol. Bioinf., 4, 403-414.
    • (2007) Comput. Biol. Bioinf , vol.4 , pp. 403-414
    • Lones, M.A.1    Tyrell, A.M.2
  • 9
    • 35048866429 scopus 로고    scopus 로고
    • A GA approach to the definition of regulatory signals in genomic sequences
    • Proc. GECCO 2004, Springer, Berlin
    • Mauri,G., Mosca,R. and Pavesi,G. (2004) A GA approach to the definition of regulatory signals in genomic sequences. Proc. GECCO 2004. LNCS 3102, Springer, Berlin, 380-391.
    • (2004) LNCS , vol.3102 , pp. 380-391
    • Mauri, G.1    Mosca, R.2    Pavesi, G.3
  • 11
    • 33750275579 scopus 로고    scopus 로고
    • Identification of weak motifs in multiple biological sequences using genetic algorithm
    • New York, ACM, pp
    • Paul,T.K. and Iba,H. (2006) Identification of weak motifs in multiple biological sequences using genetic algorithm. In: Proceedings of GECCO 2006. New York, ACM, pp. 271-278.
    • (2006) Proceedings of GECCO , pp. 271-278
    • Paul, T.K.1    Iba, H.2
  • 12
    • 33745611139 scopus 로고    scopus 로고
    • GAME: Detecting cis-regulatory elements using a genetic algorithm
    • Wei,Z. and Jensen,S.T. (2006) GAME: Detecting cis-regulatory elements using a genetic algorithm. Bioinformatics, 22, 1577-1584.
    • (2006) Bioinformatics , vol.22 , pp. 1577-1584
    • Wei, Z.1    Jensen, S.T.2
  • 13
    • 38849109559 scopus 로고    scopus 로고
    • TFBS identification based on genetic algorithm with combined representations and adaptive post-processing
    • Chan,T.-M., Leung,K.-S. and Lee,K.-H. (2008) TFBS identification based on genetic algorithm with combined representations and adaptive post-processing. Bioinformatics, 24, 341-349.
    • (2008) Bioinformatics , vol.24 , pp. 341-349
    • Chan, T.-M.1    Leung, K.-S.2    Lee, K.-H.3
  • 14
    • 33947717251 scopus 로고    scopus 로고
    • MotifCombinator: A web-based tool to search for combinations of cis-regulatory motifs
    • Kato,M. and Tsunoda,T. (2007) MotifCombinator: A web-based tool to search for combinations of cis-regulatory motifs. BMC Bioinformatics 8, 100.
    • (2007) BMC Bioinformatics , vol.8 , pp. 100
    • Kato, M.1    Tsunoda, T.2
  • 15
    • 0036137323 scopus 로고    scopus 로고
    • A higher-order background model improves detection of promoter regulatory elements by Gibbs sampling
    • Thijs,G., Lescot,M., Marchal,K., Rombauts,S., De Moor,B., Rouzé,P. and Moreau,Y. (2001) A higher-order background model improves detection of promoter regulatory elements by Gibbs sampling. Bioinformatics, 17, 1113-1122.
    • (2001) Bioinformatics , vol.17 , 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
  • 16
    • 0031603909 scopus 로고    scopus 로고
    • Calculating the exact probability of language-like patterns in biomolecular sequences
    • Atteson,K. (1998) Calculating the exact probability of language-like patterns in biomolecular sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 17-24.
    • (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.6 , pp. 17-24
    • Atteson, K.1
  • 17
    • 0033289316 scopus 로고    scopus 로고
    • An exact method for finding short motifs in sequences with application to the ribosome binding site problem
    • Tompa,M. (1999) An exact method for finding short motifs in sequences with application to the ribosome binding site problem. Proc. Int. Conf. Intell. Syst. Mol. Biol., 7, 262-271.
    • (1999) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.7 , pp. 262-271
    • Tompa, M.1
  • 18
    • 0032413411 scopus 로고    scopus 로고
    • Predicting gene regulatory elements in silico on a genomic scale
    • Brazma,A., Jonassen,I., Vilo,J. and Ukkonen,E. (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res., 8, 1202-1215.
    • (1998) Genome Res , vol.8 , pp. 1202-1215
    • Brazma, A.1    Jonassen, I.2    Vilo, J.3    Ukkonen, E.4
  • 19
    • 0034708338 scopus 로고    scopus 로고
    • Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals
    • Vanet,A., Marsan,L., Labigne,A. and Sagot,M.F. (2000) Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals. J. Mol. Biol., 297, 335-353.
    • (2000) J. Mol. Biol , vol.297 , pp. 335-353
    • Vanet, A.1    Marsan, L.2    Labigne, A.3    Sagot, M.F.4
  • 20
    • 0035187203 scopus 로고    scopus 로고
    • Combining frequency and positional information to predict transcription factor binding sites
    • Kielbasa,S.M., Korbel,J.O., Beule,D., Schuchhardt,J. and Herzel,H. (2001) Combining frequency and positional information to predict transcription factor binding sites. Bioinformatics., 17, 1019-1026.
    • (2001) Bioinformatics , vol.17 , pp. 1019-1026
    • Kielbasa, S.M.1    Korbel, J.O.2    Beule, D.3    Schuchhardt, J.4    Herzel, H.5
  • 21
    • 0025320805 scopus 로고
    • An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • Lawrence,C.E. and Reilly,A.A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins, 7, 41-51.
    • (1990) Proteins , vol.7 , pp. 41-51
    • Lawrence, C.E.1    Reilly, A.A.2
  • 22
  • 23
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • Bailey,T. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Mach. Learn., 21 51-80.
    • (1995) Mach. Learn , vol.21 , pp. 51-80
    • Bailey, T.1    Elkan, C.2
  • 24
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
    • (2000) J. Mol. Biol , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 25
    • 0029144601 scopus 로고
    • Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
    • Neuwald,A.F., Liu,J.S. and Lawrence,C.E. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci. 4, 1618-1632.
    • (1995) Protein Sci , vol.4 , pp. 1618-1632
    • Neuwald, A.F.1    Liu, J.S.2    Lawrence, C.E.3
  • 26
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequence clustered by whole genome mRNA quantitation
    • Roth,F.P., Hughes,J.D., Estep,P.W. and Church,G.M. (1998) Finding DNA regulatory motifs within unaligned noncoding sequence clustered by whole genome mRNA quantitation. Nat. Biotechol., 16, 939-945.
    • (1998) Nat. Biotechol , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 27
    • 29144442902 scopus 로고    scopus 로고
    • Alignments anchored on genomic landmarks can aid in the identification of regulatory elements
    • Tharakaraman,K., Mariño-Ramírez,L., Sheetlin,S., Landsman,D. and Spouge,J.L. (2005) Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics, 21(Suppl. 1), i440-i448.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Tharakaraman, K.1    Mariño-Ramírez, L.2    Sheetlin, S.3    Landsman, D.4    Spouge, J.L.5
  • 28
    • 53749093398 scopus 로고    scopus 로고
    • Seeder: Discriminative seeding DNA motif discovery
    • Fauteux,F., Blanchette,M. and Strömvik,M.V. (2008) Seeder: discriminative seeding DNA motif discovery. Bioinformatics, 24 2303-2307.
    • (2008) Bioinformatics , vol.24 , pp. 2303-2307
    • Fauteux, F.1    Blanchette, M.2    Strömvik, M.V.3
  • 29
    • 3142737815 scopus 로고    scopus 로고
    • Discovery of sequence motifs related to coexpression of genes using evolutionary computation
    • Fogel,G.B., Weekes,D.G., Varga,G., Dow,E.R., Harlow,H.B., Onyia,J.E. and Su.,C. (2004) Discovery of sequence motifs related to coexpression of genes using evolutionary computation. Nucleic Acids Res., 32 3826-3835.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3826-3835
    • Fogel, G.B.1    Weekes, D.G.2    Varga, G.3    Dow, E.R.4    Harlow, H.B.5    Onyia, J.E.6    Su, C.7
  • 30
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootten,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
    • (1996) Methods Enzymol , vol.266 , pp. 554-571
    • Wootten, J.C.1    Federhen, S.2
  • 33
    • 0023821516 scopus 로고
    • Identification of a putative regulator of early T cell activation genes
    • Shaw,J.P., Utz,P.J., Durand,D.B., Toole,J.J., Emmel,E.A. and Crabtree,G.R. (1988) Identification of a putative regulator of early T cell activation genes. Science, 241, 202-205.
    • (1988) Science , vol.241 , pp. 202-205
    • Shaw, J.P.1    Utz, P.J.2    Durand, D.B.3    Toole, J.J.4    Emmel, E.A.5    Crabtree, G.R.6
  • 34
    • 0037208166 scopus 로고    scopus 로고
    • Matys,V., Fricke,E., Ge?ers,R., Gösling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC®: Transcriptional regulation, from pattern to profiles. Nucleic Acids Res., 31, 374-378.
    • Matys,V., Fricke,E., Ge?ers,R., Gösling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC®: Transcriptional regulation, from pattern to profiles. Nucleic Acids Res., 31, 374-378.
  • 35
    • 0033532171 scopus 로고    scopus 로고
    • Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells
    • Kel,A., Kel-Margoulis,O., Babenko,V. and Wingender,E. (1999) Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells. J. Mol. Biol., 288, 353-376.
    • (1999) J. Mol. Biol , vol.288 , pp. 353-376
    • Kel, A.1    Kel-Margoulis, O.2    Babenko, V.3    Wingender, E.4
  • 36
    • 0028971143 scopus 로고
    • MatInd and MatInspector - new fast and versatile tools for detection of consensus matches in nucleotide sequence data
    • Quandt,K., Frech,K., Karas,H., Wingender,E. and Werner,T. (1995) MatInd and MatInspector - new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
    • (1995) Nucleic Acids Res , vol.23 , pp. 4878-4884
    • Quandt, K.1    Frech, K.2    Karas, H.3    Wingender, E.4    Werner, T.5
  • 37
  • 39
    • 0034879323 scopus 로고    scopus 로고
    • Genomic organization and promoter analysis of human KCNN3 gene
    • Sun,G., Tomita,H., Shakkottai,V.G. and Gargus,J.J. (2001) Genomic organization and promoter analysis of human KCNN3 gene. J. Hum. Genet., 46, 463-470.
    • (2001) J. Hum. Genet , vol.46 , pp. 463-470
    • Sun, G.1    Tomita, H.2    Shakkottai, V.G.3    Gargus, J.J.4
  • 40
    • 2342599054 scopus 로고    scopus 로고
    • Exercise and myocyte enhancer factor 2 regulation in human skeletal muscle
    • McGee,S.L. and Hargreaves,M. (2004) Exercise and myocyte enhancer factor 2 regulation in human skeletal muscle. Diabetes, 53, 1208-1214.
    • (2004) Diabetes , vol.53 , pp. 1208-1214
    • McGee, S.L.1    Hargreaves, M.2
  • 41
    • 2442442938 scopus 로고    scopus 로고
    • Myocyte enhancer factor 2 mediates calcium-dependent transcription of the interleukin-2 gene in T lymphocytes: A calcium signaling module that is distinct from but collaborates with the nuclear factor of activated T cells (NFAT)
    • Pan,F., Ye,Z., Cheng,L. and Liu,J.O. (2004) Myocyte enhancer factor 2 mediates calcium-dependent transcription of the interleukin-2 gene in T lymphocytes: A calcium signaling module that is distinct from but collaborates with the nuclear factor of activated T cells (NFAT). J. Biol. Chem., 279, 14477-14480.
    • (2004) J. Biol. Chem , vol.279 , pp. 14477-14480
    • Pan, F.1    Ye, Z.2    Cheng, L.3    Liu, J.O.4
  • 42
    • 0033954325 scopus 로고    scopus 로고
    • COMPEL: A database on composite regulatory elements providing combinatorial transcriptional regulation
    • Kel-Margoulis,O.V., Romashchenko,A.G., Kolchanov,N.A., Wingender,E. and Kel,A.E. (2000) COMPEL: A database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res., 28, 311-315.
    • (2000) Nucleic Acids Res , vol.28 , pp. 311-315
    • Kel-Margoulis, O.V.1    Romashchenko, A.G.2    Kolchanov, N.A.3    Wingender, E.4    Kel, A.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.