메뉴 건너뛰기




Volumn 37, Issue SUPPL. 2, 2009, Pages

RegAnalyst: A web interface for the analysis of regulatory motifs, networks and pathways

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

EID: 67849126823     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp388     Document Type: Article
Times cited : (9)

References (38)
  • 1
    • 0036532201 scopus 로고    scopus 로고
    • Deciphering gene expression regulatory networks
    • Wyrick,J.J. and Young,R.A. (2002) Deciphering gene expression regulatory networks. Curr. Opin. Genet. Dev., 12, 130-136.
    • (2002) Curr. Opin. Genet. Dev , vol.12 , pp. 130-136
    • Wyrick, J.J.1    Young, R.A.2
  • 2
    • 0030927867 scopus 로고    scopus 로고
    • Searching for regulatory elements in human noncoding sequences
    • Duret,L. and Bucher,P. (1997) Searching for regulatory elements in human noncoding sequences. Curr. Opin. Struct. Biol., 7, 399-406.
    • (1997) Curr. Opin. Struct. Biol , vol.7 , pp. 399-406
    • Duret, L.1    Bucher, P.2
  • 3
    • 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
  • 4
    • 0036277075 scopus 로고    scopus 로고
    • Functional genomics as applied to mapping transcription regulatory networks
    • Banerjee,N. and Zhang,M.Q. (2002) Functional genomics as applied to mapping transcription regulatory networks. Curr. Opin. Microbiol., 5, 313-317.
    • (2002) Curr. Opin. Microbiol , vol.5 , pp. 313-317
    • Banerjee, N.1    Zhang, M.Q.2
  • 5
    • 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
  • 6
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 7
    • 33645748095 scopus 로고    scopus 로고
    • What are DNA sequence motifs?
    • D'Haeseleer,P. (2006) What are DNA sequence motifs? Nat. Biotechnol. 24, 423-425.
    • (2006) Nat. Biotechnol , vol.24 , pp. 423-425
    • D'Haeseleer, P.1
  • 8
    • 26444584579 scopus 로고    scopus 로고
    • Limitations and potentials of current motif discovery algorithms
    • Hu,J., Li,B. and Kihara,D. (2005) Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res., 33, 4899-4913.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4899-4913
    • Hu, J.1    Li, B.2    Kihara, D.3
  • 9
    • 0242559076 scopus 로고    scopus 로고
    • Applying signal theory to the analysis of biomolecules
    • Kauer,G. and Blocker,H. (2003) Applying signal theory to the analysis of biomolecules. Bioinformatics, 19, 2016-2021.
    • (2003) Bioinformatics , vol.19 , pp. 2016-2021
    • Kauer, G.1    Blocker, H.2
  • 11
    • 0037566452 scopus 로고    scopus 로고
    • Expression analysis of a tyrosinase promoter sequence in zebrafish
    • Camp,E., Badhwar,P., Mann,G.J. and Lardelli,M. (2003) Expression analysis of a tyrosinase promoter sequence in zebrafish. Pigment Cell Res., 16, 117-126.
    • (2003) Pigment Cell Res , vol.16 , pp. 117-126
    • Camp, E.1    Badhwar, P.2    Mann, G.J.3    Lardelli, M.4
  • 12
    • 0042825331 scopus 로고    scopus 로고
    • A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c ( dosR or devR) for expression
    • Florczyk,M.A., McCue,L.A., Purkayastha,A., Currenti,E., Wolin,M.J. and McDonough,K.A. (2003) A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c ( dosR or devR) for expression. Infect. Immun., 71, 5332-5343.
    • (2003) Infect. Immun , vol.71 , pp. 5332-5343
    • Florczyk, M.A.1    McCue, L.A.2    Purkayastha, A.3    Currenti, E.4    Wolin, M.J.5    McDonough, K.A.6
  • 14
    • 0242521361 scopus 로고    scopus 로고
    • Upstream short sequence repeats regulate expression of the alpha C protein of group B Streptococcus
    • Puopolo,K.M. and Mado.,L.C. (2003) Upstream short sequence repeats regulate expression of the alpha C protein of group B Streptococcus. Mol. Microbiol., 50, 977-991.
    • (2003) Mol. Microbiol , vol.50 , pp. 977-991
    • Puopolo, K.M.1    Mado, L.C.2
  • 17
    • 67849083518 scopus 로고    scopus 로고
    • Gomez,M. and Smith,I. (2000) In Hatfull,G.F. and Jacobs,W.R. Jr (eds), Molecular genetics of Mycobacteria. ASM Press, Washington, DC, pp. 111-129.
    • Gomez,M. and Smith,I. (2000) In Hatfull,G.F. and Jacobs,W.R. Jr (eds), Molecular genetics of Mycobacteria. ASM Press, Washington, DC, pp. 111-129.
  • 18
    • 0034780485 scopus 로고    scopus 로고
    • Nonreplicating persistence of Mycobacterium tuberculosis
    • Wayne,L.G. and Sohaskey,C.D. (2001) Nonreplicating persistence of Mycobacterium tuberculosis. Annu. Rev. Microbiol., 55, 139-163.
    • (2001) Annu. Rev. Microbiol , vol.55 , pp. 139-163
    • Wayne, L.G.1    Sohaskey, C.D.2
  • 21
    • 3142727129 scopus 로고    scopus 로고
    • Spectral Repeat Finder (SRF): Identification of repetitive sequences using Fourier transformation
    • Sharma,D., Issac,B., Raghava,G.P. and Ramaswamy,R. (2004) Spectral Repeat Finder (SRF): Identification of repetitive sequences using Fourier transformation. Bioinformatics, 20, 1405-1412.
    • (2004) Bioinformatics , vol.20 , pp. 1405-1412
    • Sharma, D.1    Issac, B.2    Raghava, G.P.3    Ramaswamy, R.4
  • 22
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 23
    • 0032954835 scopus 로고    scopus 로고
    • Transcription of two sigma 70 homologue genes, sigA and sigB, in stationary-phase Mycobacterium tuberculosis
    • Hu,Y. and Coates,A.R. (1999) Transcription of two sigma 70 homologue genes, sigA and sigB, in stationary-phase Mycobacterium tuberculosis. J. Bacteriol., 181, 469-476.
    • (1999) J. Bacteriol , vol.181 , pp. 469-476
    • Hu, Y.1    Coates, A.R.2
  • 24
    • 0042905768 scopus 로고    scopus 로고
    • YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation
    • Sinha,S. and Tompa,M. (2003) YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 31, 3586-3588.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3586-3588
    • Sinha, S.1    Tompa, M.2
  • 25
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • van Helden,J., Andre,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281, 827-842.
    • (1998) J. Mol. Biol , vol.281 , pp. 827-842
    • van Helden, J.1    Andre, B.2    Collado-Vides, J.3
  • 26
    • 33747823564 scopus 로고    scopus 로고
    • MEME: Discovering and analyzing DNA and protein sequence motifs
    • Bailey,T.L., Williams,N., Misleh,C. and Li,W.W. (2006) MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res., 34, W369-W373.
    • (2006) Nucleic Acids Res , vol.34
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4
  • 27
    • 33745320292 scopus 로고    scopus 로고
    • Bounded search for de novo identification of degenerate cis-regulatory elements
    • Carlson,J.M., Chakravarty,A., Khetani,R.S. and Gross,R.H. (2006) Bounded search for de novo identification of degenerate cis-regulatory elements. BMC Bioinformatics, 7, 254.
    • (2006) BMC Bioinformatics , vol.7 , pp. 254
    • Carlson, J.M.1    Chakravarty, A.2    Khetani, R.S.3    Gross, R.H.4
  • 29
    • 0027986926 scopus 로고
    • Functional analysis of transcription of the Mycobacterium tuberculosis 16S rDNA-encoding gene
    • Verma,A., Kinger,A.K. and Tyagi,J.S. (1994) Functional analysis of transcription of the Mycobacterium tuberculosis 16S rDNA-encoding gene. Gene, 148, 113-118.
    • (1994) Gene , vol.148 , pp. 113-118
    • Verma, A.1    Kinger, A.K.2    Tyagi, J.S.3
  • 31
    • 0004279283 scopus 로고    scopus 로고
    • Oxford University Press, New York, pp
    • Lewin,B. (1997) Genes VI. Oxford University Press, New York, pp. 847-883.
    • (1997) Genes VI , pp. 847-883
    • Lewin, B.1
  • 32
    • 29244443682 scopus 로고    scopus 로고
    • Transcription and autoregulation of the Rv3134c-devR-devS operon of Mycobacterium tuberculosis
    • Bagchi,G., Chauhan,S., Sharma,D. and Tyagi,J.S. (2005) Transcription and autoregulation of the Rv3134c-devR-devS operon of Mycobacterium tuberculosis. Microbiology, 151, 4045-4053.
    • (2005) Microbiology , vol.151 , pp. 4045-4053
    • Bagchi, G.1    Chauhan, S.2    Sharma, D.3    Tyagi, J.S.4
  • 33
    • 0029747225 scopus 로고    scopus 로고
    • A study of mycobacterial transcriptional apparatus: Identification of novel features in promoter elements
    • Bashyam,M.D., Kaushal,D., Dasgupta,S.K. and Tyagi,A.K. (1996) A study of mycobacterial transcriptional apparatus: Identification of novel features in promoter elements. J. Bacteriol., 178, 4847-4853.
    • (1996) J. Bacteriol , vol.178 , pp. 4847-4853
    • Bashyam, M.D.1    Kaushal, D.2    Dasgupta, S.K.3    Tyagi, A.K.4
  • 34
    • 44949128202 scopus 로고    scopus 로고
    • Cooperative binding of phosphorylated DevR to upstream sites is necessary and sufficient for activation of the Rv3134c-devRS operon in Mycobacterium tuberculosis: Implication in the induction of DevR target genes
    • Chauhan,S. and Tyagi,J.S. (2008) Cooperative binding of phosphorylated DevR to upstream sites is necessary and sufficient for activation of the Rv3134c-devRS operon in Mycobacterium tuberculosis: implication in the induction of DevR target genes. J. Bacteriol., 190, 4301-4312.
    • (2008) J. Bacteriol , vol.190 , pp. 4301-4312
    • Chauhan, S.1    Tyagi, J.S.2
  • 35
    • 48149089000 scopus 로고    scopus 로고
    • Interaction of DevR with multiple binding sites synergistically activates divergent transcription of narK2-Rv1738 genes in Mycobacterium tuberculosis
    • Chauhan,S. and Tyagi,J.S. (2008) Interaction of DevR with multiple binding sites synergistically activates divergent transcription of narK2-Rv1738 genes in Mycobacterium tuberculosis. J. Bacteriol. 190, 5394-5403.
    • (2008) J. Bacteriol , vol.190 , pp. 5394-5403
    • Chauhan, S.1    Tyagi, J.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.