메뉴 건너뛰기




Volumn 43, Issue W1, 2015, Pages W50-W56

RSAT 2015: Regulatory sequence analysis tools

(18)  Medina Rivera, Alejandra a   Defrance, Matthieu b   Sand, Olivier c,d   Herrmann, Carl e,f,g,p   Castro Mondragon, Jaime A e,p   Delerce, Jeremy e,p   Jaeger, Sébastien e,h   Blanchet, Christophe i   Vincens, Pierre e,j,k   Caron, Christophe l,p   Staines, Daniel M m   Contreras Moreira, Bruno n,o   Artufel, Marie e,p   Charbonnier Khamvongsa, Lucie e,p   Hernandez, Céline e,j,k   Thieffry, Denis e,j,k   Thomas Chollier, Morgane e,j,k   Van Helden, Jacques b,e,p  

d France   (France)
e INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; EPIGENETICS; GENE EXPRESSION; GENE SEQUENCE; GENETIC VARIATION; GENOMICS; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY SEQUENCE ANALYSIS TOOL; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; BINDING SITE; COMPUTER PROGRAM; INTERNET; METABOLISM; NUCLEOTIDE MOTIF; REGULATORY SEQUENCE;

EID: 84979857821     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv362     Document Type: Article
Times cited : (208)

References (28)
  • 1
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • van Helden, J., André, 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    André, B.2    Collado-Vides, J.3
  • 2
    • 0034731822 scopus 로고    scopus 로고
    • A web site for the computational analysis of yeast regulatory sequences
    • van Helden, J., Collado-Vides, J., André, B. and Andr, B. (2000) A web site for the computational analysis of yeast regulatory sequences. Yeast, 16, 177-187.
    • (2000) Yeast , vol.16 , pp. 177-187
    • Van Helden, J.1    Collado-Vides, J.2    André, B.3    Andr, B.4
  • 3
    • 0041620271 scopus 로고    scopus 로고
    • Regulatory sequence analysis tools
    • van Helden, J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res., 31, 3593-3596.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3593-3596
    • Van Helden, J.1
  • 6
    • 70349989504 scopus 로고    scopus 로고
    • Retrieve-ensembl-seq: User-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
    • Sand, O., Thomas-Chollier, M. and van Helden, J. (2009) Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. Bioinformatics, 25, 2739-2740.
    • (2009) Bioinformatics , vol.25 , pp. 2739-2740
    • Sand, O.1    Thomas-Chollier, M.2    Van Helden, J.3
  • 7
    • 0034656326 scopus 로고    scopus 로고
    • Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
    • van Helden, J., Rios, A.F. and Collado-Vides, J. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res., 28, 1808-1818.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1808-1818
    • Van Helden, J.1    Rios, A.F.2    Collado-Vides, J.3
  • 8
    • 0034651804 scopus 로고    scopus 로고
    • Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
    • van Helden, J., del Olmo, M. and Pérez-Ortín, J.E. (2000) Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res., 28, 1000-1010.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1000-1010
    • Van Helden, J.1    Del Olmo, M.2    Pérez-Ortín, J.E.3
  • 10
    • 84864425198 scopus 로고    scopus 로고
    • A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs
    • Thomas-Chollier, M., Darbo, E., Herrmann, C., Defrance, M., Thieffry, D. and van Helden, J. (2012) A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat. Protoc., 7, 1551-1568.
    • (2012) Nat. Protoc. , vol.7 , pp. 1551-1568
    • Thomas-Chollier, M.1    Darbo, E.2    Herrmann, C.3    Defrance, M.4    Thieffry, D.5    Van Helden, J.6
  • 11
    • 52749097035 scopus 로고    scopus 로고
    • Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
    • Turatsinze, J.-V., Thomas-Chollier, M., Defrance, M. and van Helden, J. (2008) Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat. Protoc., 3, 1578-1588.
    • (2008) Nat. Protoc. , vol.3 , pp. 1578-1588
    • Turatsinze, J.-V.1    Thomas-Chollier, M.2    Defrance, M.3    Van Helden, J.4
  • 17
    • 39749171239 scopus 로고    scopus 로고
    • Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
    • Janky, R. and van Helden, J. (2008) Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics, 9, 37.
    • (2008) BMC Bioinformatics , vol.9 , pp. 37
    • Janky, R.1    Van Helden, J.2
  • 21
    • 84892758927 scopus 로고    scopus 로고
    • Footprint DB: A database of transcription factors with annotated cis elements and binding interfaces
    • Sebastian, A. and Contreras-Moreira, B. (2014) footprint DB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics, 30, 258-265.
    • (2014) Bioinformatics , vol.30 , pp. 258-265
    • Sebastian, A.1    Contreras-Moreira, B.2
  • 23
    • 36548999724 scopus 로고    scopus 로고
    • Discovery of conserved motifs in promoters of orthologous genes in prokaryotes
    • Janky, R. and van Helden, J. (2007) Discovery of conserved motifs in promoters of orthologous genes in prokaryotes. Methods Mol. Biol., 395, 293-308.
    • (2007) Methods Mol. Biol. , vol.395 , pp. 293-308
    • Janky, R.1    Van Helden, J.2
  • 24
    • 36549062896 scopus 로고    scopus 로고
    • Discovery of motifs in promoters of coregulated genes
    • Sand, O. and van Helden, J. (2007) Discovery of motifs in promoters of coregulated genes. Methods Mol. Biol., 395, 329-348.
    • (2007) Methods Mol. Biol. , vol.395 , pp. 329-348
    • Sand, O.1    Van Helden, J.2
  • 26
    • 52749092937 scopus 로고    scopus 로고
    • Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences
    • Defrance, M., Janky, R., Sand, O. and van Helden, J. (2008) Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat. Protoc., 3, 1589-1603.
    • (2008) Nat. Protoc. , vol.3 , pp. 1589-1603
    • Defrance, M.1    Janky, R.2    Sand, O.3    Van Helden, J.4
  • 27
    • 52749085084 scopus 로고    scopus 로고
    • Analyzing multiple data sets by interconnecting RSAT programs via SOAPWeb services: An example with ChIP-chip data
    • Sand, O., Thomas-Chollier, M., Vervisch, E. and van Helden, J. (2008) Analyzing multiple data sets by interconnecting RSAT programs via SOAPWeb services: an example with ChIP-chip data. Nat. Protoc., 3, 1604-1615.
    • (2008) Nat. Protoc. , vol.3 , pp. 1604-1615
    • Sand, O.1    Thomas-Chollier, M.2    Vervisch, E.3    Van Helden, J.4
  • 28
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J., Nekrutenko, A., Taylor, J. and Galaxy Team (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
    • (2010) Genome Biol. , vol.11 , pp. R86
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3    Team, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.