메뉴 건너뛰기




Volumn 25, Issue 12, 2009, Pages 1521-1527

Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 66349129690     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp235     Document Type: Article
Times cited : (17)

References (35)
  • 1
    • 0033536012 scopus 로고    scopus 로고
    • Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
    • Alon,U. et al. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl Acad. Sci. USA, 96, 6745-6750.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 6745-6750
    • Alon, U.1
  • 2
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 3
    • 84864994884 scopus 로고    scopus 로고
    • Iterative signature algorithm for the analysis of large-scale gene expression data
    • Bergmann,S. et al. (2003) Iterative signature algorithm for the analysis of large-scale gene expression data. Phys Rev. E Stat. Nonlin. Soft. Matter Phys, 67, 031902.
    • (2003) Phys Rev. E Stat. Nonlin. Soft. Matter Phys , vol.67 , pp. 031902
    • Bergmann, S.1
  • 4
    • 0033031790 scopus 로고    scopus 로고
    • Data analysis and integration: Of steps and arrows
    • Bittner,M. et al. (1999) Data analysis and integration: Of steps and arrows. Nat. Genet., 22, 213-215.
    • (1999) Nat. Genet , vol.22 , pp. 213-215
    • Bittner, M.1
  • 5
    • 0034564271 scopus 로고    scopus 로고
    • Analysis of gene expression microarrays for phenotype classification
    • Califano,A. et al. (2000) Analysis of gene expression microarrays for phenotype classification. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8, 75-85.
    • (2000) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.8 , pp. 75-85
    • Califano, A.1
  • 6
    • 33750367972 scopus 로고    scopus 로고
    • Latent Kaposi's sarcoma-associated herpesvirus infection of endothelial cells activates hypoxia-induced factors
    • Carroll,P.A. et al. (2006) Latent Kaposi's sarcoma-associated herpesvirus infection of endothelial cells activates hypoxia-induced factors. J. Virol., 80, 10802-10812.
    • (2006) J. Virol , vol.80 , pp. 10802-10812
    • Carroll, P.A.1
  • 8
    • 0038005018 scopus 로고    scopus 로고
    • DAVID: Database for Annotation, Visualization, and Integrated Discovery
    • Dennis,G. et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol., 4, P3.
    • (2003) Genome Biol , vol.4
    • Dennis, G.1
  • 9
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen,M.B. et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95 14863-14868.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 14863-14868
    • Eisen, M.B.1
  • 10
    • 33847044392 scopus 로고    scopus 로고
    • Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation
    • Fuhrken,P.G. et al. (2007) Comparative, genome-scale transcriptional analysis of CHRF-288-11 and primary human megakaryocytic cell cultures provides novel insights into lineage-specific differentiation. Exp. Hematol., 35, 476-489.
    • (2007) Exp. Hematol , vol.35 , pp. 476-489
    • Fuhrken, P.G.1
  • 11
    • 0141682147 scopus 로고    scopus 로고
    • Productive lytic replication of a recombinant Kaposi's sarcoma-associated herpesvirus in efficient primary infection of primary human endothelial cells
    • Gao,S.J. et al. (2003) Productive lytic replication of a recombinant Kaposi's sarcoma-associated herpesvirus in efficient primary infection of primary human endothelial cells. J. Virol., 77, 9738-9749.
    • (2003) J. Virol , vol.77 , pp. 9738-9749
    • Gao, S.J.1
  • 12
    • 0037057374 scopus 로고    scopus 로고
    • Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
    • RESEARCH0059
    • Gasch,A.P. and Eisen,M.B. (2002) Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol., 3, RESEARCH0059.
    • (2002) Genome Biol , vol.3
    • Gasch, A.P.1    Eisen, M.B.2
  • 13
    • 0034710876 scopus 로고    scopus 로고
    • Coupled two-way clustering analysis of gene microarray data
    • Getz,G. et al. (2000) Coupled two-way clustering analysis of gene microarray data. Proc. Natl Acad. Sci. USA, 97, 12079-12084.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 12079-12084
    • Getz, G.1
  • 14
    • 84927511887 scopus 로고
    • Direct clustering of a data matrix
    • Hartigan,J.A. (1972) Direct clustering of a data matrix. J. Am. Stat. Assoc. (JASA), 67, 123-129.
    • (1972) J. Am. Stat. Assoc. (JASA) , vol.67 , pp. 123-129
    • Hartigan, J.A.1
  • 15
    • 0036699526 scopus 로고    scopus 로고
    • Revealing modular organization in the yeast transcriptional network
    • Ihmels,J. et al. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet., 31, 370-377.
    • (2002) Nat. Genet , vol.31 , pp. 370-377
    • Ihmels, J.1
  • 16
    • 14644416505 scopus 로고    scopus 로고
    • Identifying time-lagged gene clusters using gene expression data
    • Ji,L. and Tan,K.L. (2005) Identifying time-lagged gene clusters using gene expression data. Bioinformatics, 21, 509-516.
    • (2005) Bioinformatics , vol.21 , pp. 509-516
    • Ji, L.1    Tan, K.L.2
  • 17
    • 38549126643 scopus 로고    scopus 로고
    • KEGG for linking genomes to life and the environment
    • Kanehisa,M. et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res., 36, D480-D484.
    • (2008) Nucleic Acids Res , vol.36
    • Kanehisa, M.1
  • 18
    • 16344370048 scopus 로고    scopus 로고
    • Finding regulatory modules through large-scale gene-expression data analysis
    • Kloster,M. et al. (2005) Finding regulatory modules through large-scale gene-expression data analysis. Bioinformatics, 21 1172-1179.
    • (2005) Bioinformatics , vol.21 , pp. 1172-1179
    • Kloster, M.1
  • 19
    • 0036012349 scopus 로고    scopus 로고
    • Plaid models for gene expression data
    • Lazzeroni,L. and Owen,A. (2002) Plaid models for gene expression data. Statist. Sinica., 12, 61-86.
    • (2002) Statist. Sinica , vol.12 , pp. 61-86
    • Lazzeroni, L.1    Owen, A.2
  • 22
    • 0042024906 scopus 로고    scopus 로고
    • A gene recommender algorithm to identify coexpressed genes in C. elegans
    • Owen,A.B. et al. (2003) A gene recommender algorithm to identify coexpressed genes in C. elegans. Genome Res., 13, 1828-1837.
    • (2003) Genome Res , vol.13 , pp. 1828-1837
    • Owen, A.B.1
  • 23
    • 33646137384 scopus 로고    scopus 로고
    • A systematic comparison and evaluation of biclustering methods for gene expression data
    • Prelic,A. et al. (2006) A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics, 22, 1122-1129.
    • (2006) Bioinformatics , vol.22 , pp. 1122-1129
    • Prelic, A.1
  • 24
    • 33847235341 scopus 로고    scopus 로고
    • Persistent activation of STAT3 by latent Kaposi's sarcoma-associated herpesvirus infection of endothelial cells
    • Punjabi,A.S. et al. (2007) Persistent activation of STAT3 by latent Kaposi's sarcoma-associated herpesvirus infection of endothelial cells. J. Virol., 81, 2449-2458.
    • (2007) J. Virol , vol.81 , pp. 2449-2458
    • Punjabi, A.S.1
  • 25
    • 33746067911 scopus 로고    scopus 로고
    • Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks
    • Reiss,D.J. et al. (2006) Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics, 7, 280.
    • (2006) BMC Bioinformatics , vol.7 , pp. 280
    • Reiss, D.J.1
  • 26
    • 4444367133 scopus 로고    scopus 로고
    • Biclustering microarray data by Gibbs sampling
    • Sheng,Q. et al. (2003) Biclustering microarray data by Gibbs sampling. Bioinformatics, 19 (Suppl 2), ii196-ii205.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Sheng, Q.1
  • 27
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
    • Spellman,P.T. et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
    • (1998) Mol. Biol. Cell , vol.9 , pp. 3273-3297
    • Spellman, P.T.1
  • 28
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian,A. et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA, 102, 15545-15550.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 29
    • 35748941236 scopus 로고    scopus 로고
    • EDISA: Extracting biclusters from multiple time-series of gene expression profiles
    • Supper,J. et al. (2007) EDISA: Extracting biclusters from multiple time-series of gene expression profiles. BMC Bioinformatics, 8 334.
    • (2007) BMC Bioinformatics , vol.8 , pp. 334
    • Supper, J.1
  • 30
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
    • Tamayo,P. et al. (1999) Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA, 96, 2907-2912.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 2907-2912
    • Tamayo, P.1
  • 31
    • 11244306358 scopus 로고    scopus 로고
    • Discovering statistically significant biclusters in gene expression data
    • Tanay,A. et al. (2002) Discovering statistically significant biclusters in gene expression data. Bioinformatics, 18 (Suppl 1), S136-S144.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Tanay, A.1
  • 32
    • 29744457034 scopus 로고    scopus 로고
    • Kaposi's sarcoma-associated herpesvirus induction of AP-1 and interleukin 6 during primary infection mediated by multiple mitogen-activated protein kinase pathways
    • Xie,J. et al. (2005) Kaposi's sarcoma-associated herpesvirus induction of AP-1 and interleukin 6 during primary infection mediated by multiple mitogen-activated protein kinase pathways. J. Virol., 79, 15027-15037.
    • (2005) J. Virol , vol.79 , pp. 15027-15037
    • Xie, J.1
  • 33
    • 34247117937 scopus 로고    scopus 로고
    • Kaposi's sarcoma-associated herpesvirus promotes angiogenesis by inducing angiopoietin-2 expression via AP-1 and Ets1
    • Ye,F.C. et al. (2007) Kaposi's sarcoma-associated herpesvirus promotes angiogenesis by inducing angiopoietin-2 expression via AP-1 and Ets1. J. Virol., 81, 3980-3991.
    • (2007) J. Virol , vol.81 , pp. 3980-3991
    • Ye, F.C.1
  • 34
    • 27644467562 scopus 로고    scopus 로고
    • Early and sustained expression of latent and host modulating genes in coordinated transcriptional program of KSHV productive primary infection of human primary endothelial cells
    • Yoo,S.M. et al. (2005) Early and sustained expression of latent and host modulating genes in coordinated transcriptional program of KSHV productive primary infection of human primary endothelial cells. Virology, 343, 47-64.
    • (2005) Virology , vol.343 , pp. 47-64
    • Yoo, S.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.