메뉴 건너뛰기




Volumn 35, Issue SUPPL.2, 2007, Pages

STAMP: A web tool for exploring DNA-binding motif similarities

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

EID: 34547569191     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm272     Document Type: Article
Times cited : (392)

References (31)
  • 1
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W. and Lenhard, B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91-D94.
    • (2004) Nucleic Acids Res. , vol.32
    • Sandelin, A.1    Alkema, W.2    Engstrom, P.3    Wasserman, W.W.4    Lenhard, B.5
  • 3
    • 23144441978 scopus 로고    scopus 로고
    • T-Reg Comparator: An analysis tool for the comparison of position weight matrices
    • Roepcke, S., Grossmann, S., Rahmann, S. and Vingron, M. (2005) T-Reg Comparator: an analysis tool for the comparison of position weight matrices. Nucleic Acids Res., 33, W438-W441.
    • (2005) Nucleic Acids Res. , vol.33
    • Roepcke, S.1    Grossmann, S.2    Rahmann, S.3    Vingron, M.4
  • 4
    • 33748931997 scopus 로고    scopus 로고
    • MACO: A gapped-alignment scoring tool for comparing transcription factor binding sites
    • Su, G., Mao, B. and Wang, J. (2006) MACO: a gapped-alignment scoring tool for comparing transcription factor binding sites. In Silico Biol., 6, 307-310.
    • (2006) Silico Biol. , vol.6 , pp. 307-310
    • Su, G.1    Mao, B.2    Wang, J.3
  • 5
    • 1842505125 scopus 로고    scopus 로고
    • Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
    • Sandelin, A. and Wasserman, W.W. (2004) Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol., 338, 207-215.
    • (2004) J. Mol. Biol. , vol.338 , pp. 207-215
    • Sandelin, A.1    Wasserman, W.W.2
  • 6
    • 32544434809 scopus 로고    scopus 로고
    • A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data
    • Macisaac, K.D., Gordon, D.B., Nekludova, L., Odom, D.T., Schreiber, J., Gifford, D.K., Young, R.A. and Fraenkel, E. (2006)A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics, 22, 423-429.
    • (2006) Bioinformatics , vol.22 , pp. 423-429
    • MacIsaac, K.D.1    Gordon, D.B.2    Nekludova, L.3    Odom, D.T.4    Schreiber, J.5    Gifford, D.K.6    Young, R.A.7    Fraenkel, E.8
  • 7
    • 34047192976 scopus 로고    scopus 로고
    • DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies
    • Mahony, S., Auron, P. and Benos, P.V. (2007) DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies. PLoS Comput Biol, 3, e61.
    • (2007) PLoS Comput Biol , vol.3
    • Mahony, S.1    Auron, P.2    Benos, P.V.3
  • 9
    • 0029789461 scopus 로고    scopus 로고
    • Searching databases of conserved sequence regions by aligning protein multiple-alignments
    • Pietrokovski, S. (1996) Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res., 24, 3836-3845.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 3836-3845
    • Pietrokovski, S.1
  • 10
    • 0344906814 scopus 로고    scopus 로고
    • Combining phylogenetic data with co-regulated genes to identify regulatory motifs
    • Wang, T. and Stormo, G.D. (2003) Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics, 19, 2369-2380.
    • (2003) Bioinformatics , vol.19 , pp. 2369-2380
    • Wang, T.1    Stormo, G.D.2
  • 11
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • Sokal, R.R. and Michener, C.D. (1958) A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull., 28, 1409-1438.
    • (1958) Univ. Kansas Sci. Bull. , vol.28 , pp. 1409-1438
    • Sokal, R.R.1    Michener, C.D.2
  • 12
    • 0031042985 scopus 로고    scopus 로고
    • Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree
    • Dopazo, J. and Carazo, J.M. (1997) Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree. J. Mol. Evol., 44, 226-233.
    • (1997) J. Mol. Evol. , vol.44 , pp. 226-233
    • Dopazo, J.1    Carazo, J.M.2
  • 15
    • 17444402501 scopus 로고    scopus 로고
    • Drosophila DNase i footprint database: A systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
    • Bergman, C.M., Carlson, J.W. and Celniker, S.E. (2005) Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics, 21, 1747-1749.
    • (2005) Bioinformatics , vol.21 , pp. 1747-1749
    • Bergman, C.M.1    Carlson, J.W.2    Celniker, S.E.3
  • 16
    • 0032573426 scopus 로고    scopus 로고
    • A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
    • Robison, K., McGuire, A.M. and Church, G.M. (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol., 284, 241-254.
    • (1998) J. Mol. Biol. , vol.284 , pp. 241-254
    • Robison, K.1    McGuire, A.M.2    Church, G.M.3
  • 18
    • 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., 127-138.
    • (2001) Pac. Symp. Biocomput. , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 19
    • 29144465554 scopus 로고    scopus 로고
    • Improved detection of DNA motifs using a self-organized clustering of familial binding motifs
    • Mahony, S., Golden, A., Smith, T.J. and Benos, P.V. (2005) Improved detection of DNA motifs using a self-organized clustering of familial binding motifs. Bioinformatics, 21, i283-i291.
    • (2005) Bioinformatics , vol.21
    • Mahony, S.1    Golden, A.2    Smith, T.J.3    Benos, P.V.4
  • 20
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
    • Liu, X.S., Brutlag, D.L. and Liu, J.S. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 21
    • 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
  • 22
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey, T.L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Pro. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
    • (1994) Pro. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 23
    • 3242884167 scopus 로고    scopus 로고
    • Weeder Web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    • Pavesi, G., Mereghetti, P., Mauri, G. and Pesole, G. (2004) Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res., 32, W199-W203.
    • (2004) Nucleic Acids Res. , vol.32
    • Pavesi, G.1    Mereghetti, P.2    Mauri, G.3    Pesole, G.4
  • 24
    • 0036137323 scopus 로고    scopus 로고
    • A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
    • Thijs, G., Lescot, M., Marchal, K., Rombauts, S., De Moor, B., Rouze, P. and Moreau, Y. (2001) A higher-order background model improves the 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    Rouze, P.6    Moreau, Y.7
  • 25
    • 0042905768 scopus 로고    scopus 로고
    • YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresen-tation
    • Sinha, S. and Tompa, M. (2003) YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresen-tation. Nucleic Acids Res., 31, 3586-3588.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3586-3588
    • Sinha, S.1    Tompa, M.2
  • 26
    • 0033655171 scopus 로고    scopus 로고
    • ANN-Spec: A method for discovering transcription factor binding sites with improved specificity
    • Workman, C.T. and Stormo, G.D. (2000) ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac. Symp. Biocomput.467-478.
    • (2000) Pac. Symp. Biocomput. , pp. 467-478
    • Workman, C.T.1    Stormo, G.D.2
  • 27
    • 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.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 28
    • 0034894539 scopus 로고    scopus 로고
    • Identifying target sites for cooperatively binding factors
    • GuhaThakurta, D. and Stormo, G.D. (2001) Identifying target sites for cooperatively binding factors. Bioinformatics, 17, 608-621.
    • (2001) Bioinformatics , vol.17 , pp. 608-621
    • Guhathakurta, D.1    Stormo, G.D.2
  • 30
    • 0000122573 scopus 로고
    • PHYLIP-Phylogeny Inference Package (Version 3.2)
    • Felsenstein, J. (1989) PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.