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Volumn 12, Issue 10, 2002, Pages 1574-1581

Judging the quality of gene expression-based clustering methods using gene annotation

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE MAPPING; GENETIC ALGORITHM; GENETIC ANALYSIS; INTERMETHOD COMPARISON; PRIORITY JOURNAL; QUALITY CONTROL; SEQUENCE HOMOLOGY;

EID: 0036798238     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.397002     Document Type: Article
Times cited : (254)

References (41)
  • 1
    • 0034098727 scopus 로고    scopus 로고
    • Systematic management and analysis of yeast gene expression data
    • Aach, J., Rindone, W., and Church, G.M. 2000. Systematic management and analysis of yeast gene expression data. Genome Res. 10: 431-445.
    • (2000) Genome Res , vol.10 , pp. 431-445
    • Aach, J.1    Rindone, W.2    Church, G.M.3
  • 2
    • 0011045178 scopus 로고    scopus 로고
    • GeneCluster. Whitehead/MIT Center for Genome Research, Cambridge, MA
    • Angelo, M. 1999. GeneCluster. Whitehead/MIT Center for Genome Research, Cambridge, MA; http:/www.genome.wi.mit.edu/cancer/software/software.html.
    • (1999)
    • Angelo, M.1
  • 4
    • 0011039573 scopus 로고    scopus 로고
    • SWIG User's Manual v.1.3
    • Beazley, D.M. 2001. SWIG User's Manual v.1.3; http://www.swig.org.
    • (2001)
    • Beazley, D.M.1
  • 5
    • 0010958196 scopus 로고    scopus 로고
    • Perl extension building with SWIG
    • O'Reilly Perl Conference 2.0, San Jose, CA
    • Beazley, D.M., Fletcher, D., and Dumont, D. 1998. Perl extension building with SWIG. In O'Reilly Perl Conference 2.0, San Jose, CA; http://www.swig.org/papers/Per198/swigperl.pdf.
    • (1998)
    • Beazley, D.M.1    Fletcher, D.2    Dumont, D.3
  • 6
    • 0036359730 scopus 로고    scopus 로고
    • A stability based method for discovering structure in clustered data
    • (eds. R.B. Altman et al.), World Scientific, Kauai, HI
    • Ben-Hur, A., Elisseeff, A., and Guyon, I. 2002. A stability based method for discovering structure in clustered data. In Pacific Symposium in Biocomputing (eds. R.B. Altman et al.), pp. 6-17. World Scientific, Kauai, HI.
    • (2002) Pacific Symposium in Biocomputing , pp. 6-17
    • Ben-Hur, A.1    Elisseeff, A.2    Guyon, I.3
  • 9
    • 0036000001 scopus 로고    scopus 로고
    • Discrimination between paralogs using microarray analysis: Application to the Yap1p and Yap2p transcriptional networks
    • Cohen, B.A., Pilpel, Y., Mitra, R.D., and Church, G.M. 2002. Discrimination between paralogs using microarray analysis: Application to the Yap1p and Yap2p transcriptional networks. Mol. Biol. Cell 13: 1608-1614.
    • (2002) Mol. Biol. Cell , vol.13 , pp. 1608-1614
    • Cohen, B.A.1    Pilpel, Y.2    Mitra, R.D.3    Church, G.M.4
  • 10
    • 0011002468 scopus 로고
    • Elements of information theory (ed. D.L. Schilling). Wiley-Interscience, New York
    • Cover, T.M. and Thomas, LA. 1991. Elements of information theory (ed. D.L. Schilling). Wiley-Interscience, New York.
    • (1991)
    • Cover, T.M.1    Thomas, L.A.2
  • 11
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi, J.L., Iyer, V.R., and Brown, P.O. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
    • (1997) Science , vol.278 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 12
    • 0010965733 scopus 로고    scopus 로고
    • Cluster
    • Eisen, M. 1999. Cluster. http://rana.lbl.gov.
    • (1999)
    • Eisen, M.1
  • 13
    • 0033031437 scopus 로고    scopus 로고
    • DNA arrays for analysis of gene expression
    • Eisen, M.B. and Brown, P.O. 1999. DNA arrays for analysis of gene expression. Methods Enzymol. 303: 179-205.
    • (1999) Methods Enzymol , vol.303 , pp. 179-205
    • Eisen, M.B.1    Brown, P.O.2
  • 14
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 95: 14863-14868.
    • (1998) Proc. Natl. Acad. Sci , vol.95 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 16
    • 0032269108 scopus 로고    scopus 로고
    • How many clusters? Which clustering method? Answers via model-based cluster analysis
    • Fraley, C. and Raftery, A.E. 1998. How many clusters? Which clustering method? Answers via model-based cluster analysis. Comput. J. 41: 578-588.
    • (1998) Comput. J , vol.41 , pp. 578-588
    • Fraley, C.1    Raftery, A.E.2
  • 18
    • 0033783651 scopus 로고    scopus 로고
    • The current excitement in bioinformatics-analysis of whole-genome expression data: How does it relate to protein structure and function?
    • Gerstein, M. and Jansen, R. 2000. The current excitement in bioinformatics-analysis of whole-genome expression data: How does it relate to protein structure and function? Curr. Opin. Struct. Biol. 10: 574-584.
    • (2000) Curr. Opin. Struct. Biol , vol.10 , pp. 574-584
    • Gerstein, M.1    Jansen, R.2
  • 19
    • 0034710876 scopus 로고    scopus 로고
    • Coupled two-way clustering analysis of gene microarray data
    • Getz, G., Levine, E., and Domany, E. 2000. Coupled two-way clustering analysis of gene microarray data. Proc. Natl. Acad. Sci. 97: 12079-12084.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 12079-12084
    • Getz, G.1    Levine, E.2    Domany, E.3
  • 22
    • 0035156258 scopus 로고    scopus 로고
    • Assessing clusters and motifs from gene expression data
    • Jakt, L.M., Cao, L., Cheah, K.S.E., and Smith, D.K. 2001. Assessing clusters and motifs from gene expression data. Genome Res. 11: 112-123.
    • (2001) Genome Res , vol.11 , pp. 112-123
    • Jakt, L.M.1    Cao, L.2    Cheah, K.S.E.3    Smith, D.K.4
  • 23
    • 0033772765 scopus 로고    scopus 로고
    • Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: RPN4 links base excision repair with proteosomes
    • Jelinsky, S., Estep, P., Church, G.M., and Samson, L. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: RPN4 links base excision repair with proteosomes. Mol. Cell. Biol. 20: 8157-8167.
    • (2000) Mol. Cell. Biol , vol.20 , pp. 8157-8167
    • Jelinsky, S.1    Estep, P.2    Church, G.M.3    Samson, L.4
  • 24
    • 0036012349 scopus 로고    scopus 로고
    • Plaid models for gene expression data
    • Lazzeroni, L. and Owen, A. 2000. Plaid models for gene expression data. Statistica Sinica 12: 61-86.
    • (2000) Statistica Sinica , vol.12 , pp. 61-86
    • Lazzeroni, L.1    Owen, A.2
  • 25
    • 0035014159 scopus 로고    scopus 로고
    • Analysis of temporal gene expression profiles: Clustering by simulated annealing and determining the optimal number of clusters
    • Lukashin, A. V. and Fuchs, R. 2001. Analysis of temporal gene expression profiles: Clustering by simulated annealing and determining the optimal number of clusters. Bioinformatics 17: 405-414.
    • (2001) Bioinformatics , vol.17 , pp. 405-414
    • Lukashin, A.V.1    Fuchs, R.2
  • 26
    • 0031616361 scopus 로고    scopus 로고
    • Cluster analysis and data visualization of large-scale gene expression data
    • (eds. R.B. Altman et al.), World Scientific, Kauai, HI
    • Michaels, G.S., Carr, D.B., Askenazi, M., Furman, S., Wen, X., and Somogyi, R. 1998. Cluster analysis and data visualization of large-scale gene expression data. In Pacific Symposium in Biocomputing (eds. R.B. Altman et al.), pp. 42-53. World Scientific, Kauai, HI.
    • (1998) Pacific Symposium in Biocomputing , pp. 42-53
    • Michaels, G.S.1    Carr, D.B.2    Askenazi, M.3    Furman, S.4    Wen, X.5    Somogyi, R.6
  • 28
    • 0035375137 scopus 로고    scopus 로고
    • Computational analysis of microarray data
    • Quackenbush, J. 2001. Computational analysis of microarray data. Nat. Rev. Genet. 2: 418-427.
    • (2001) Nat. Rev. Genet , vol.2 , pp. 418-427
    • Quackenbush, J.1
  • 29
    • 0034705202 scopus 로고    scopus 로고
    • The yeast A kinases differentially regulate iron uptake and respiratory functions
    • Robertson, L.S., Causton, H.C., Young, R.A., and Fink, G.R. 2000. The yeast A kinases differentially regulate iron uptake and respiratory functions. Proc. Natl. Acad. Sci. 97: 5984-5988.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 5984-5988
    • Robertson, L.S.1    Causton, H.C.2    Young, R.A.3    Fink, G.R.4
  • 30
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    • Roth, F.P., Hughes, J.D., Estep, P.W., and Church, G.M. 1998. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotech. 16: 939-945.
    • (1998) Nat. Biotech , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 31
    • 2642681950 scopus 로고    scopus 로고
    • Information theory primer
    • Schneider, T.D. 2000. Information theory primer. http://www.lecb.ncifcrf.gov/~toms/paper/primer.
    • (2000)
    • Schneider, T.D.1
  • 32
    • 0034565041 scopus 로고    scopus 로고
    • CLICK: A clustering algorithm with applications to gene expression analysis
    • Shamir, R. and Sharan, R. 2000. CLICK: A clustering algorithm with applications to gene expression analysis. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8: 307-316.
    • (2000) Proc. Int. Conf. Intell. Syst. Mol. Biol , vol.8 , pp. 307-316
    • Shamir, R.1    Sharan, R.2
  • 33
    • 0036133934 scopus 로고    scopus 로고
    • Clustering based on conditional distributions in an auxiliary space
    • Sinkkonen, J. and Kaski, S. 2002. Clustering based on conditional distributions in an auxiliary space. Neur. Comput. 14: 217-239.
    • (2002) Neur. Comput , vol.14 , pp. 217-239
    • Sinkkonen, J.1    Kaski, S.2
  • 34
    • 0010958817 scopus 로고    scopus 로고
    • Perl data language user guide
    • Soeller, C. and Lukka, T. 1997. Perl data language user guide. http://pdl.perl.org/.
    • (1997)
    • Soeller, C.1    Lukka, T.2
  • 36
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
    • Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitarbeewan, S., Dmitrovsky, E., Lander, E.S., and Golub, T.R. 1999. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. 96: 2907-2912.
    • (1999) Proc. Natl. Acad. Sci , vol.96 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitarbeewan, S.5    Dmitrovsky, E.6    Lander, E.S.7    Golub, T.R.8
  • 41
    • 0035024021 scopus 로고    scopus 로고
    • Validating clustering for gene expression data
    • Yeung, K.Y., Haynor, D.R., and Ruzzo, W.L. 2001. Validating clustering for gene expression data. Bioinformatics 17: 309-318.
    • (2001) Bioinformatics , vol.17 , pp. 309-318
    • Yeung, K.Y.1    Haynor, D.R.2    Ruzzo, W.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.