메뉴 건너뛰기




Volumn 2014, Issue , 2014, Pages

YTRP: A repository for yeast transcriptional regulatory pathways

Author keywords

[No Author keywords available]

Indexed keywords

NITROGEN;

EID: 84906542076     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau014     Document Type: Article
Times cited : (19)

References (28)
  • 2
    • 31544482407 scopus 로고    scopus 로고
    • Mapping pathways and phenotypes by systematic gene overexpression
    • Sopko, R., Huang, D., Preston, N. et al. (2006) Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell, 21, 319-330.
    • (2006) Mol. Cell , vol.21 , pp. 319-330
    • Sopko, R.1    Huang, D.2    Preston, N.3
  • 3
    • 34247629588 scopus 로고    scopus 로고
    • Genetic reconstruction of a functional transcriptional regulatory network
    • Hu, Z., Killion, P.J. and Iyer, V.R. (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat. Genet., 39, 683-687.
    • (2007) Nat. Genet. , vol.39 , pp. 683-687
    • Hu, Z.1    Killion, P.J.2    Iyer, V.R.3
  • 4
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of DNA binding proteins
    • Ren, B., Robert, F., Wyrick, J.J. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306.
    • (2000) Science , vol.290 , pp. 2306
    • Ren, B.1    Robert, F.2    Wyrick, J.J.3
  • 5
    • 67650663220 scopus 로고    scopus 로고
    • Backup in gene regulatory networks explains differences between binding and knockout results
    • Gitter, A., Siegfried, Z., Klutstein, M. et al. (2009) Backup in gene regulatory networks explains differences between binding and knockout results. Mol. Syst. Biol., 5, 276.
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 276
    • Gitter, A.1    Siegfried, Z.2    Klutstein, M.3
  • 6
    • 84864930280 scopus 로고    scopus 로고
    • Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data
    • Yang, T.-H. and Wu, W.-S. (2012) Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. BMC Syst. Biol., 6, 102.
    • (2012) BMC Syst. Biol. , vol.6 , pp. 102
    • Yang, T.-H.1    Wu, W.-S.2
  • 7
    • 78651272522 scopus 로고    scopus 로고
    • YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in saccharomyces cerevisiae through a web services interface
    • Abdulrehman, D., Monteiro, P.T., Teixeira, M.C. et al. (2011) YEASTRACT: providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface. Nucleic Acids Res., 39, D136-D140.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D136-D140
    • Abdulrehman, D.1    Monteiro, P.T.2    Teixeira, M.C.3
  • 8
    • 84891806965 scopus 로고    scopus 로고
    • The YEASTRACT database: An upgraded information system for the analysis of gene and genomic transcription regulation in saccharomyces cerevisiae
    • Teixeira, M.C., Monteiro, P.T., Guerreiro, J.F. et al. (2014) The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae. Nucleic Acids Res., 42, D161-D166.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D161-D166
    • Teixeira, M.C.1    Monteiro, P.T.2    Guerreiro, J.F.3
  • 11
    • 0036790999 scopus 로고    scopus 로고
    • Transitive functional annotation by shortest-path analysis of gene expression data
    • Zhou, X., Kao, M.C.J. and Wong, W.H. (2002) Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl Acad. Sci. USA, 99, 12783.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99
    • Zhou, X.1    Kao, M.C.J.2    Wong, W.H.3
  • 12
    • 67249148362 scopus 로고    scopus 로고
    • Exploring network structure, dynamics, and function using NetworkX
    • Varoquaux, G., Vaught, T. and Millman, J. (eds) Pasadena, CA USA
    • Hagberg, A., Swart, P. and Schult, D. (2008) Exploring Network Structure, Dynamics, and Function Using NetworkX. In: Varoquaux, G., Vaught, T. and Millman, J. (eds), Proceedings of the 7th Python in Science conference (SciPy 2008), Pasadena, CA USA. pp. 11-15.
    • (2008) Proceedings of the 7th Python in Science Conference (SciPy 2008) , pp. 11-15
    • Hagberg, A.1    Swart, P.2    Schult, D.3
  • 13
    • 84867453337 scopus 로고    scopus 로고
    • Graphviz-open source graph drawing tools
    • Springer, New York
    • Ellson, J., Gansner, E., Koutsofios, L. et al. (2002) Graphviz-open source graph drawing tools. In: Graph Drawing. Springer, New York, pp. 483-485.
    • (2002) Graph Drawing , pp. 483-485
    • Ellson, J.1    Gansner, E.2    Koutsofios, L.3
  • 14
    • 36448940491 scopus 로고    scopus 로고
    • New insights into the regulation of the saccharomyces cerevisiae UGA4 gene: Two parallel pathways participate in carbon-regulated transcription
    • Luzzani, C., Cardillo, S.B., Moretti, M.B. et al. (2007) New insights into the regulation of the Saccharomyces cerevisiae UGA4 gene: two parallel pathways participate in carbon-regulated transcription. Microbiology, 153, 3677-3684.
    • (2007) Microbiology , vol.153 , pp. 3677-3684
    • Luzzani, C.1    Cardillo, S.B.2    Moretti, M.B.3
  • 15
    • 9144257282 scopus 로고    scopus 로고
    • The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
    • Ruepp, A., Zollner, A., Maier, D. et al. (2004) The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res., 32, 5539-5545.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 5539-5545
    • Ruepp, A.1    Zollner, A.2    Maier, D.3
  • 16
    • 77949477875 scopus 로고    scopus 로고
    • Characterizing regulatory path motifs in integrated networks using perturbational data
    • Joshi, A., van Parys, T., Peer, Y.V. et al. (2010) Characterizing regulatory path motifs in integrated networks using perturbational data. Genome Biol., 11, R32.
    • (2010) Genome Biol. , vol.11 , pp. R32
    • Joshi, A.1    Van Parys, T.2    Peer, Y.V.3
  • 17
    • 70350452746 scopus 로고    scopus 로고
    • Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks
    • Huang, S.C. and Fraenkel, E. (2009) Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci. Signal., 2, ra40.
    • (2009) Sci. Signal. , vol.2 , pp. ra40
    • Huang, S.C.1    Fraenkel, E.2
  • 18
    • 34547830859 scopus 로고    scopus 로고
    • SPINE: A framework for signaling-regulatory pathway inference from cause-effect experiments
    • Ourfali, O., Shlomi, T., Ideker, T. et al. (2007) SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics, 23, i359-i366.
    • (2007) Bioinformatics , vol.23 , pp. i359-i366
    • Ourfali, O.1    Shlomi, T.2    Ideker, T.3
  • 19
    • 42949096140 scopus 로고    scopus 로고
    • EQED: An efficient method for interpreting eQTL associations using protein networks
    • Suthram, S., Beyer, A., Karp, R.M. et al. (2008) eQED: an efficient method for interpreting eQTL associations using protein networks. Mol. Syst. Biol., 4, 162.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 162
    • Suthram, S.1    Beyer, A.2    Karp, R.M.3
  • 20
    • 61349114190 scopus 로고    scopus 로고
    • Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
    • Yeger-Lotem, E., Riva, L., Su, L.J. et al. (2009) Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity. Nat. Genet., 41, 316-323.
    • (2009) Nat. Genet. , vol.41 , pp. 316-323
    • Yeger-Lotem, E.1    Riva, L.2    Su, L.J.3
  • 22
    • 79959930131 scopus 로고    scopus 로고
    • ChIP-array: Combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor
    • Qin, J., Li, M.J., Wang, P. et al. (2011) ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res., 39, W430-W436.
    • (2011) Nucleic Acids Res. , vol.39 , pp. W430-W436
    • Qin, J.1    Li, M.J.2    Wang, P.3
  • 24
    • 28444475160 scopus 로고    scopus 로고
    • A data integration methodology for systems biology
    • Hwang, D., Rust, A.G., Ramsey, S. et al. (2005) A data integration methodology for systems biology. Proc. Natl Acad. Sci. USA, 102, 17296-17301.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 17296-17301
    • Hwang, D.1    Rust, A.G.2    Ramsey, S.3
  • 25
    • 28444498336 scopus 로고    scopus 로고
    • A data integration methodology for systems biology: Experimental verification
    • Hwang, D., Smith, J.J., Leslie, D.M. et al. (2005) A data integration methodology for systems biology: experimental verification. Proc. Natl Acad. Sci. USA, 102, 17302-17307.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 17302-17307
    • Hwang, D.1    Smith, J.J.2    Leslie, D.M.3
  • 26
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe, N.M., Babu, M.M., Yu, H. et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1    Babu, M.M.2    Yu, H.3
  • 27
    • 67650093251 scopus 로고    scopus 로고
    • The yeast GATA factor gat1 occupies a central position in nitrogen catabolite repression-sensitive gene activation
    • Georis, I., Feller, A., Vierendeels, F. et al. (2009) The yeast GATA factor Gat1 occupies a central position in nitrogen catabolite repression-sensitive gene activation. Mol. Cell. Biol., 29, 3803-3815.
    • (2009) Mol. Cell. Biol. , vol.29 , pp. 3803-3815
    • Georis, I.1    Feller, A.2    Vierendeels, F.3
  • 28
    • 0030944694 scopus 로고    scopus 로고
    • Cross regulation of four GATA factors that control nitrogen catabolic gene expression in saccharomyces cerevisiae
    • Coffman, J.A., Rai, R., Loprete, D.M. et al. (1997) Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae. J. Bacteriol., 179, 3416-3429.
    • (1997) J. Bacteriol. , vol.179 , pp. 3416-3429
    • Coffman, J.A.1    Rai, R.2    Loprete, D.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.