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Volumn 5, Issue 7, 2004, Pages

From co-expression to co-regulation: how many microarray experiments do we need?

Author keywords

Additional Data File; Cluster Algorithm; Gene Subset; Microarray Dataset; Microarray Experiment

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; CLUSTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; METHODOLOGY; SACCHAROMYCES CEREVISIAE; STATISTICS;

EID: 4844229238     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2004-5-7-r48     Document Type: Article
Times cited : (81)

References (35)
  • 1
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • PID: 9843981, COI: 1:CAS:528:DyaK1cXotVGmurk%3D
    • Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Nat Acad Sci USA. 1998, 95: 14863-14868. 10.1073/pnas.95.25.14863. DOI: 10.1073/pnas.95.25.14863
    • (1998) Proc Nat Acad Sci USA , vol.95 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3    Botstein, D.4
  • 3
    • 0036649020 scopus 로고    scopus 로고
    • Large-scale prediction of Saccharomyces cerevisiaegene function using overlapping transcriptional clusters
    • PID: 12089522, COI: 1:CAS:528:DC%2BD38XkvVGmtL8%3D
    • Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R, Altschuler SJ: Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat Genet. 2002, 31: 255-265. 10.1038/ng906. DOI: 10.1038/ng906
    • (2002) Nat Genet , vol.31 , pp. 255-265
    • Wu, L.F.1    Hughes, T.R.2    Davierwala, A.P.3    Robinson, M.D.4    Stoughton, R.5    Altschuler, S.J.6
  • 4
    • 0036532201 scopus 로고    scopus 로고
    • Deciphering gene expression regulatory networks
    • PID: 11893484, COI: 1:CAS:528:DC%2BD38XhvVCnsLY%3D
    • Wyrick JJ, Young RA: Deciphering gene expression regulatory networks. Curr Opin Genet Dev. 2002, 12: 130-136. 10.1016/S0959-437X(02)00277-0. DOI: 10.1016/S0959-437X(02)00277-0
    • (2002) Curr Opin Genet Dev , vol.12 , pp. 130-136
    • Wyrick, J.J.1    Young, R.A.2
  • 5
    • 0031742022 scopus 로고    scopus 로고
    • Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiaeby microarray hybridization
    • PID: 9843569, COI: 1:CAS:528:DyaK1cXnvFOmt7Y%3D
    • Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell. 1998, 9: 3273-3297. DOI: 10.1091/mbc.9.12.3273
    • (1998) Mol Biol Cell , vol.9 , pp. 3273-3297
    • Spellman, P.T.1    Sherlock, G.2    Zhang, M.Q.3    Iyer, V.R.4    Anders, K.5    Eisen, M.B.6    Brown, P.O.7    Botstein, D.8    Futcher, B.9
  • 6
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • PID: 10391217, COI: 1:CAS:528:DyaK1MXkt1eqsbY%3D
    • Tavazoie S, Huges JD, Campbell MJ, Cho RJ, Church GM: Systematic determination of genetic network architecture. Nat Genet. 1999, 22: 281-285. 10.1038/10343. DOI: 10.1038/10343
    • (1999) Nat Genet , vol.22 , pp. 281-285
    • Tavazoie, S.1    Huges, J.D.2    Campbell, M.J.3    Cho, R.J.4    Church, G.M.5
  • 7
    • 0038703409 scopus 로고    scopus 로고
    • Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein
    • PID: 12743294, COI: 1:CAS:528:DC%2BD3sXktV2ns74%3D
    • Geiss GK, Carter VS, He Y, Kwieciszewski BK, Holzman T, Korth MJ, Lazaro CA, Fausto N, Bumgarner RE, Katze MG: Gene expression profiling of the cellular transcriptional network regulated by alpha/beta interferon and its partial attenuation by the hepatitis C virus nonstructural 5A protein. J Virol. 2003, 77: 6367-6375. 10.1128/JVI.77.11.6367-6375.2003. DOI: 10.1128/JVI.77.11.6367-6375.2003
    • (2003) J Virol , vol.77 , pp. 6367-6375
    • Geiss, G.K.1    Carter, V.S.2    He, Y.3    Kwieciszewski, B.K.4    Holzman, T.5    Korth, M.J.6    Lazaro, C.A.7    Fausto, N.8    Bumgarner, R.E.9    Katze, M.G.10
  • 8
    • 0035252126 scopus 로고    scopus 로고
    • Identification and analysis of eukaryotic promoters: recent computational approaches
    • PID: 11173099, COI: 1:CAS:528:DC%2BD3MXhtFaktbw%3D
    • Ohler U, Niemann H: Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet. 2001, 17: 56-60. 10.1016/S0168-9525(00)02174-0. DOI: 10.1016/S0168-9525(00)02174-0
    • (2001) Trends Genet , vol.17 , pp. 56-60
    • Ohler, U.1    Niemann, H.2
  • 9
    • 0032848435 scopus 로고    scopus 로고
    • Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae
    • PID: 10447512, COI: 1:CAS:528:DyaK1MXls1yhu7k%3D
    • Wolfsberg TG, Gabrielian AE, Campbell MJ, Cho RJ, Spouge JL, Landsman D: Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Res. 1999, 9: 775-792.
    • (1999) Genome Res , vol.9 , pp. 775-792
    • Wolfsberg, T.G.1    Gabrielian, A.E.2    Campbell, M.J.3    Cho, R.J.4    Spouge, J.L.5    Landsman, D.6
  • 10
    • 0033772765 scopus 로고    scopus 로고
    • Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiaecells: Rpn4 links base excision repair with proteasomes
    • PID: 11027285, COI: 1:CAS:528:DC%2BD3cXnslOjtrk%3D
    • Jelinsky SA, Estep P, Church GM, Samson LD: Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol. 2000, 20: 8157-8167. 10.1128/MCB.20.21.8157-8167.2000. DOI: 10.1128/MCB.20.21.8157-8167.2000
    • (2000) Mol Cell Biol , vol.20 , pp. 8157-8167
    • Jelinsky, S.A.1    Estep, P.2    Church, G.M.3    Samson, L.D.4
  • 11
    • 0032861774 scopus 로고    scopus 로고
    • SCPD: a promoter database of the yeast Saccharomyces cerevisiae
    • PID: 10487868, COI: 1:CAS:528:DyaK1MXntVWitbs%3D
    • Zhu J, Zhang MQ: SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics. 1999, 15: 607-611. 10.1093/bioinformatics/15.7.607. DOI: 10.1093/bioinformatics/15.7.607
    • (1999) Bioinformatics , vol.15 , pp. 607-611
    • Zhu, J.1    Zhang, M.Q.2
  • 12
    • 0033968614 scopus 로고    scopus 로고
    • The yeast proteome database (YPD) and Caenorhabditis elegansproteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information
    • PID: 10592185, COI: 1:CAS:528:DC%2BD3cXhvVKjsrw%3D
    • Costanzo MC, Hogan JD, Cusick ME, Davis BP, Fancher AM, Hodges PE, Kondu P, Lengieza C, Lew-Smith JE, Lingner C, et al: The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res. 2000, 28: 73-76. 10.1093/nar/28.1.73. DOI: 10.1093/nar/28.1.73
    • (2000) Nucleic Acids Res , vol.28 , pp. 73-76
    • Costanzo, M.C.1    Hogan, J.D.2    Cusick, M.E.3    Davis, B.P.4    Fancher, A.M.5    Hodges, P.E.6    Kondu, P.7    Lengieza, C.8    Lew-Smith, J.E.9    Lingner, C.10
  • 15
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • PID: 11102521, COI: 1:CAS:528:DC%2BD3cXovFansbw%3D
    • Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO: Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell. 2000, 11: 4241-4257. DOI: 10.1091/mbc.11.12.4241
    • (2000) Mol Biol Cell , vol.11 , pp. 4241-4257
    • Gasch, A.P.1    Spellman, P.T.2    Kao, C.M.3    Carmel-Harel, O.4    Eisen, M.B.5    Storz, G.6    Botstein, D.7    Brown, P.O.8
  • 16
    • 0035162698 scopus 로고    scopus 로고
    • Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p
    • PID: 11598186, COI: 1:CAS:528:DC%2BD3MXns1Chsbg%3D
    • Gasch AP, Huang M, Metzner S, Botstein D, Elledge SJ, Brown PO: Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol Biol Cell. 2001, 12: 2987-3003. DOI: 10.1091/mbc.12.10.2987
    • (2001) Mol Biol Cell , vol.12 , pp. 2987-3003
    • Gasch, A.P.1    Huang, M.2    Metzner, S.3    Botstein, D.4    Elledge, S.J.5    Brown, P.O.6
  • 17
    • 22844453564 scopus 로고    scopus 로고
    • MCLUST: Software for model-based cluster analysis
    • Fraley C, Raftery AE: MCLUST: Software for model-based cluster analysis. J Classification. 1999, 16: 297-306. 10.1007/s003579900058. DOI: 10.1007/s003579900058
    • (1999) J Classification , vol.16 , pp. 297-306
    • Fraley, C.1    Raftery, A.E.2
  • 18
    • 0032269108 scopus 로고    scopus 로고
    • How many clusters? Which clustering method? - Answers via model-based cluster analysis
    • Fraley C, Raftery AE: How many clusters? Which clustering method? - Answers via model-based cluster analysis. Computer J. 1998, 41: 578-588. DOI: 10.1093/comjnl/41.8.578
    • (1998) Computer J , vol.41 , pp. 578-588
    • Fraley, C.1    Raftery, A.E.2
  • 19
    • 0035998835 scopus 로고    scopus 로고
    • Model-based clustering, discriminant analysis, and density estimation
    • Fraley C, Raftery AE: Model-based clustering, discriminant analysis, and density estimation. J Am Stat Assoc. 2002, 97: 611-631. 10.1198/016214502760047131. DOI: 10.1198/016214502760047131
    • (2002) J Am Stat Assoc , vol.97 , pp. 611-631
    • Fraley, C.1    Raftery, A.E.2
  • 20
    • 0037667290 scopus 로고    scopus 로고
    • Clustering gene expression data with repeated measurements
    • PID: 12734014
    • Yeung KY, Medvedovic M, Bumgarner RE: Clustering gene expression data with repeated measurements. Genome Biol. 2003, 4: R34-10.1186/gb-2003-4-5-r34. DOI: 10.1186/gb-2003-4-5-r34
    • (2003) Genome Biol , vol.4 , pp. R34
    • Yeung, K.Y.1    Medvedovic, M.2    Bumgarner, R.E.3
  • 21
    • 3042686005 scopus 로고    scopus 로고
    • Bayesian mixture model based clustering of replicated microarray data
    • PID: 14871871, COI: 1:CAS:528:DC%2BD2cXkt1Srtb4%3D
    • Medvedovic M, Yeung KY, Bumgarner R: Bayesian mixture model based clustering of replicated microarray data. Bioinformatics. 2004, 20: 1222-1232. 10.1093/bioinformatics/bth068. DOI: 10.1093/bioinformatics/bth068
    • (2004) Bioinformatics , vol.20 , pp. 1222-1232
    • Medvedovic, M.1    Yeung, K.Y.2    Bumgarner, R.3
  • 22
    • 0036739286 scopus 로고    scopus 로고
    • Bayesian infinite mixture model based clustering of gene expression profiles
    • PID: 12217911, COI: 1:CAS:528:DC%2BD38XmvVCqsb4%3D
    • Medvedovic M, Sivaganesan S: Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics. 2002, 18: 1194-1206. 10.1093/bioinformatics/18.9.1194. DOI: 10.1093/bioinformatics/18.9.1194
    • (2002) Bioinformatics , vol.18 , pp. 1194-1206
    • Medvedovic, M.1    Sivaganesan, S.2
  • 23
    • 0034782618 scopus 로고    scopus 로고
    • Model-based clustering and data transformations for gene expression data
    • PID: 11673243, COI: 1:CAS:528:DC%2BD3MXot1Ggu7Y%3D
    • Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL: Model-based clustering and data transformations for gene expression data. Bioinformatics. 2001, 17: 977-987. 10.1093/bioinformatics/17.10.977. DOI: 10.1093/bioinformatics/17.10.977
    • (2001) Bioinformatics , vol.17 , pp. 977-987
    • Yeung, K.Y.1    Fraley, C.2    Murua, A.3    Raftery, A.E.4    Ruzzo, W.L.5
  • 27
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • PID: 11206552, COI: 1:CAS:528:DC%2BD3MXpvVeqsg%3D%3D
    • Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO: Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 2001, 409: 533-538. 10.1038/35054095. DOI: 10.1038/35054095
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3    Botstein, D.4    Snyder, M.5    Brown, P.O.6
  • 30
    • 0003410791 scopus 로고    scopus 로고
    • Springer-Verlag, Berlin
    • Kohonen T: Self-organizing maps. 1997, Berlin: Springer-Verlag DOI: 10.1007/978-3-642-97966-8
    • (1997) Self-organizing maps
    • Kohonen, T.1
  • 31
    • 0001457509 scopus 로고
    • Some methods for classification and analysis of multivariate observations
    • Cam LML, Neyman J, (eds), University of California Press, Berkeley
    • MacQueen J: Some methods for classification and analysis of multivariate observations. In Proceedings of the 5th Berkeley Symposium on Mathematical Statistics and Probability. Edited by: Cam LML, Neyman J. 1965, Berkeley: University of California Press, 281-297.
    • (1965) In Proceedings of the 5th Berkeley Symposium on Mathematical Statistics and Probability , pp. 281-297
    • MacQueen, J.1
  • 33
    • 0036203115 scopus 로고    scopus 로고
    • A mixture model-based approach to the clustering of microarray expression data
    • PID: 11934740, COI: 1:CAS:528:DC%2BD38XivFKrsrs%3D
    • McLachlan GJ, Bean RW, Peel D: A mixture model-based approach to the clustering of microarray expression data. Bioinformatics. 2002, 18: 413-422. 10.1093/bioinformatics/18.3.413. DOI: 10.1093/bioinformatics/18.3.413
    • (2002) Bioinformatics , vol.18 , pp. 413-422
    • McLachlan, G.J.1    Bean, R.W.2    Peel, D.3
  • 34
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation
    • PID: 10077610, COI: 1:CAS:528:DyaK1MXhvFyks7k%3D
    • Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR: Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Nat Acad Sci USA. 1999, 96: 2907-2912. 10.1073/pnas.96.6.2907. DOI: 10.1073/pnas.96.6.2907
    • (1999) Proc Nat Acad Sci USA , vol.96 , pp. 2907-2912
    • Tamayo, P.1    Slonim, D.2    Mesirov, J.3    Zhu, Q.4    Kitareewan, S.5    Dmitrovsky, E.6    Lander, E.S.7    Golub, T.R.8


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