메뉴 건너뛰기




Volumn 90, Issue 11, 2002, Pages 1722-1742

Functional bioinformatics of microarray data: From expression to regulation

Author keywords

Adaptive quality based clustering; Clustering; Gibbs sampling; Microarray; Motif finding; Regulation

Indexed keywords

ALGORITHMS; BIOTECHNOLOGY; DNA; GENES; SAMPLING;

EID: 0013224530     PISSN: 00189219     EISSN: None     Source Type: Journal    
DOI: 10.1109/JPROC.2002.804681     Document Type: Article
Times cited : (37)

References (61)
  • 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
    • U. Alon, N. Barkai, D. A. Notterman, K. Gish, S. Ybarra, D. Mack, and A. J. Levine, "Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays," in Proc. Natl. Acad. Sci. USA, vol. 96, 1999, pp. 6745-6750.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 6745-6750
    • Alon, U.1    Barkai, N.2    Notterman, D.A.3    Gish, K.4    Ybarra, S.5    Mack, D.6    Levine, A.J.7
  • 2
    • 0036191191 scopus 로고    scopus 로고
    • A cluster validity framework for genome expression data
    • F. Azuaje, "A cluster validity framework for genome expression data," Bioinformatics, vol. 18, pp. 319-320, 2002.
    • (2002) Bioinformatics , vol.18 , pp. 319-320
    • Azuaje, F.1
  • 3
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • T. L. Bailey and C. Elkan, "Unsupervised learning of multiple motifs in biopolymers using expectation maximization," Machine Learning, vol. 21, pp. 51-80, 1995.
    • (1995) Machine Learning , vol.21 , pp. 51-80
    • Bailey, T.L.1    Elkan, C.2
  • 4
    • 0034833408 scopus 로고    scopus 로고
    • Class discovery in gene expression data
    • A. Ben-Dor, N. Friedman, and Z. Yakhini, "Class discovery in gene expression data," in Proc. 5th Annu. Conf. Comput. Mol. Biol., 2001, pp. 31-38.
    • (2001) Proc. , vol.5 , pp. 31-38
    • Ben-Dor, A.1    Friedman, N.2    Yakhini, Z.3
  • 5
    • 0032728081 scopus 로고    scopus 로고
    • Clustering gene expression patterns
    • A. Ben-Dor, R. Shamir, and Z. Yakhini, "Clustering gene expression patterns," J. Comput. Biol., vol. 6, pp. 281-297, 1999.
    • (1999) J. Comput. Biol. , vol.6 , pp. 281-297
    • Ben-Dor, A.1    Shamir, R.2    Yakhini, Z.3
  • 7
    • 0033150947 scopus 로고    scopus 로고
    • Regulatory elements and expression profiles
    • P. Bucher, "Regulatory elements and expression profiles," Current Opinion in Structural Biol., vol. 9, pp. 400-407, 1999.
    • (1999) Current Opinion in Structural Biol. , vol.9 , pp. 400-407
    • Bucher, P.1
  • 8
    • 0026602181 scopus 로고
    • Expectation maximization for identifying protein-binding sites with variable lengths from unaligned DNA fragments
    • L. R. Cardon and G. D. Stormo, "Expectation maximization for identifying protein-binding sites with variable lengths from unaligned DNA fragments," J. Mol. Biol., vol. 223, pp. 159-170, 1992.
    • (1992) J. Mol. Biol. , vol.223 , pp. 159-170
    • Cardon, L.R.1    Stormo, G.D.2
  • 10
    • 0036080361 scopus 로고    scopus 로고
    • Adaptive quality-based clustering of gene expression profiles
    • F. De Smet, J. Mathys, K. Marchal, G. Thijs, B. De Moor, and Y. Moreau, "Adaptive quality-based clustering of gene expression profiles," Bioinformatics, vol. 18, no. 5, pp. 735-746, 2002.
    • (2002) Bioinformatics , vol.18 , Issue.5 , pp. 735-746
    • De Smet, F.1    Mathys, J.2    Marchal, K.3    Thijs, G.4    De Moor, B.5    Moreau, Y.6
  • 12
    • 84984934477 scopus 로고    scopus 로고
    • Expression profiling using cDNA microarrays
    • D. J. Duggan, M. Bittner, Y. Chen, P. Meltzer, and J. M. Trent, "Expression profiling using cDNA microarrays," Nature Genetics, vol. 21, no. 1 Suppl., pp. 10-14, 1999.
    • (1999) Nature Genetics , vol.21 , Issue.1 SUPPL. , pp. 10-14
    • Duggan, D.J.1    Bittner, M.2    Chen, Y.3    Meltzer, P.4    Trent, J.M.5
  • 13
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • M. B. Eisen, P. T. Spellman, P. O. Brown, and D. Botstein, "Cluster analysis and display of genome-wide expression patterns," in Proc. Nat. Acad. Sci. USA, vol. 95, 1998, pp. 14863-14868.
    • (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
  • 14
    • 22844453564 scopus 로고    scopus 로고
    • MCLUST: Software for model-based cluster analysis
    • C. Fraley and E. Raftery, "MCLUST: Software for model-based cluster analysis," J. Classification, vol. 16, pp. 297-306, 1999.
    • (1999) J. Classification , vol.16 , pp. 297-306
    • Fraley, C.1    Raftery, E.2
  • 15
    • 0036188158 scopus 로고    scopus 로고
    • Mixture modeling of gene expression data from microarray experiments
    • D. Ghosh and A. M. Chinnaiyan, "Mixture modeling of gene expression data from microarray experiments," Bioinformatics, vol. 18, pp. 275-286, 2002.
    • (2002) Bioinformatics , vol.18 , pp. 275-286
    • Ghosh, D.1    Chinnaiyan, A.M.2
  • 16
    • 0034894539 scopus 로고    scopus 로고
    • Identifying target sites for co-operatively binding factors
    • D. GuhaThakurta and G. D. Stormo, "Identifying target sites for co-operatively binding factors," Bioinformatics, vol. 17, pp. 608-621, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 608-621
    • Guhathakurta, D.1    Stormo, G.D.2
  • 18
    • 0035108235 scopus 로고    scopus 로고
    • A hierarchical Unsupervised growing neural network for clustering gene expression patterns
    • J. Herrero, A. Valencia, and J. Dopazo, "A hierarchical Unsupervised growing neural network for clustering gene expression patterns," Bioinformatics, vol. 17, pp. 126-136, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 126-136
    • Herrero, J.1    Valencia, A.2    Dopazo, J.3
  • 19
    • 0025372992 scopus 로고
    • Identification of consensus patterns in unaligned DNA sequences known to be functionally related
    • G. Z. Hertz, G. W. Hartzell, and G. D. Stormo, "Identification of consensus patterns in unaligned DNA sequences known to be functionally related," Comput. Appl. Biosci., vol. 6, pp. 81-92, 1990.
    • (1990) Comput. Appl. Biosci. , vol.6 , pp. 81-92
    • Hertz, G.Z.1    Hartzell, G.W.2    Stormo, G.D.3
  • 20
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • G. Z. Hertz and G. D. Stormo, "Identifying DNA and protein patterns with statistically significant alignments of multiple sequences," Bioinformatics, vol. 15, no. 7/8, pp. 563-577, 1999.
    • (1999) Bioinformatics , vol.15 , Issue.7-8 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 21
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: Identification and analysis of coexpressed genes
    • L. J. Heyer, S. Kruglyak, and S. Yooseph, "Exploring expression data: Identification and analysis of coexpressed genes," Genome Res., vol. 9, pp. 1106-1115, 1999.
    • (1999) Genome Res. , vol.9 , pp. 1106-1115
    • Heyer, L.J.1    Kruglyak, S.2    Yooseph, S.3
  • 22
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • J. D. Hughes, P. W. Estep, S. Tavazoie, and G. M. Church, "Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae" J. Mol. Biol., vol. 296, pp. 1205-1214, 2000.
    • (2000) J. Mol. Biol. , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 23
    • 0035375137 scopus 로고    scopus 로고
    • Computational analysis of microarray data
    • J. Quackenbush, "Computational analysis of microarray data," Nat. Rev. Genetics, vol. 2, pp. 418-427, 2001.
    • (2001) Nat. Rev. Genetics , vol.2 , pp. 418-427
    • Quackenbush, J.1
  • 25
    • 0035979259 scopus 로고    scopus 로고
    • Bootstrap cluster analysis: Assessing the reliability of conclusions from microarray experiments
    • M. K. Kerr and G. A. Churchill, "Bootstrap cluster analysis: Assessing the reliability of conclusions from microarray experiments," Proc. Nat. Acad. Sci. USA, vol. 98, pp. 8961-8965, 2001.
    • (2001) Proc. Nat. Acad. Sci. USA , vol.98 , pp. 8961-8965
    • Kerr, M.K.1    Churchill, G.A.2
  • 27
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • C. E. Lawrence, S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald, and J. C. Wootton, "Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment," Science, vol. 262, pp. 208-214, 1993.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 28
    • 0025320805 scopus 로고
    • An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • C. E. Lawrence and A. A. Reilly, "An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences," Proteins, vol. 7, pp. 41-51, 1990.
    • (1990) Proteins , vol.7 , pp. 41-51
    • Lawrence, C.E.1    Reilly, A.A.2
  • 29
    • 0036085047 scopus 로고    scopus 로고
    • PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silica analysis of promoter sequences
    • M. Lescot, P. Déhais, G. Thijs, K. Marchal, Y. Moreau, Y. Van de Peer, P. Rouzé, and S. Rombauts, "PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silica analysis of promoter sequences," Nucleic Acids Res., vol. 30, pp. 325-327, 2002.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 325-327
    • Lescot, M.1    Déhais, P.2    Thijs, G.3    Marchal, K.4    Moreau, Y.5    Van De Peer, Y.6    Rouzé, P.7    Rombauts, S.8
  • 31
    • 79951870792 scopus 로고
    • The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem
    • J. S. Liu, "The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem," J. Amer. Statist. Assoc., vol. 89, no. 427, pp. 958-966, 1994.
    • (1994) J. Amer. Statist. Assoc. , vol.89 , Issue.427 , pp. 958-966
    • Liu, J.S.1
  • 32
    • 0033059370 scopus 로고    scopus 로고
    • Bayesian inference on biopolymer models
    • J. S. Liu and C. E. Lawrence, "Bayesian inference on biopolymer models," Bioinformatics, vol. 15, pp. 38-52, 1999.
    • (1999) Bioinformatics , vol.15 , pp. 38-52
    • Liu, J.S.1    Lawrence, C.E.2
  • 33
    • 84950424966 scopus 로고
    • Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
    • J. S. Liu, A. F. Neuwald, and C. E. Lawrence, "Bayesian models for multiple local sequence alignment and Gibbs sampling strategies," J. Amer. Statist. Assoc., vol. 90, no. 432, pp. 1156-1170, 1995.
    • (1995) J. Amer. Statist. Assoc. , vol.90 , Issue.432 , pp. 1156-1170
    • Liu, J.S.1    Neuwald, A.F.2    Lawrence, C.E.3
  • 34
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • X. Liu, D. L. Brutlag, and J. S. Liu, "BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes," in Proc. Pacific Symp. Biocomputing, vol. 6, 2001, pp. 127-138.
    • (2001) Proc. Pacific Symp. Biocomputing , vol.6 , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 35
    • 0035014159 scopus 로고    scopus 로고
    • Analysis of temporal gene expression profiles: Clustering by simulated annealing and determining the optimal number of clusters
    • A. V. Lukashin and R. Fuchs, "Analysis of temporal gene expression profiles: Clustering by simulated annealing and determining the optimal number of clusters," Bioinformatics, vol. 17, pp. 405-414, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 405-414
    • Lukashin, A.V.1    Fuchs, R.2
  • 36
    • 0033677426 scopus 로고    scopus 로고
    • Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification
    • L. Marsan and M.-F. Sagot, "Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification," J. Comp. Biol., vol. 7, pp. 345-360, 2000.
    • (2000) J. Comp. Biol. , vol.7 , pp. 345-360
    • Marsan, L.1    Sagot, M.-F.2
  • 40
    • 0035252126 scopus 로고    scopus 로고
    • Identification and analysis of eukaryotic promoters: Recent computational approaches
    • U. Ohler and H. Niemann, "Identification and analysis of eukaryotic promoters: Recent computational approaches," Trends in Genetics, vol. 17, no. 2, pp. 56-60, 2001.
    • (2001) Trends in Genetics , vol.17 , Issue.2 , pp. 56-60
    • Ohler, U.1    Niemann, H.2
  • 41
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole genome mRNA quantitation
    • F. P. Roth, J. D. Hughes, P. W. Estep, and G. M. Church, "Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole genome mRNA quantitation," Nature Biotech., vol. 16, pp. 939-945, 1998.
    • (1998) Nature Biotech. , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 42
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • G. Schwarz, "Estimating the dimension of a model," Ann. Statist., vol. 6, pp. 461-464, 1978.
    • (1978) Ann. Statist. , vol.6 , pp. 461-464
    • Schwarz, G.1
  • 43
    • 0034062083 scopus 로고    scopus 로고
    • Analysis of large-scale gene expression data
    • G. Sherlock, "Analysis of large-scale gene expression data," Current Opinion in Immunology, vol. 12, pp. 201-205, 2000.
    • (2000) Current Opinion in Immunology , vol.12 , pp. 201-205
    • Sherlock, G.1
  • 44
    • 0033027794 scopus 로고    scopus 로고
    • Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
    • P. Tamayo, D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E. S. Lander, and T. R. Golub, "Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation," Proc. Nat. Acad. Sci. USA, vol. 96, pp. 2907-2912, 1999.
    • (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
  • 45
    • 84950758368 scopus 로고
    • The calculation of posterior distributions by data augmentation
    • M. A. Tanner and W. H. Wong, "The calculation of posterior distributions by data augmentation (with discussion)," J. Amer. Statist. Assoc., vol. 82, no. 398, pp. 528-550, 1987.
    • (1987) J. Amer. Statist. Assoc. , vol.82 , Issue.398 , pp. 528-550
    • Tanner, M.A.1    Wong, W.H.2
  • 46
  • 47
    • 0036137323 scopus 로고    scopus 로고
    • A higher order background model improves the detection of promoter regulatory elements by Gibbs sampling
    • G. Thijs, M. Lescot, K. Marchal, S. Rombauts, B. De Moor, P. Rouzé, and Y. Moreau, "A higher order background model improves the detection of promoter regulatory elements by Gibbs sampling," Bioinformatics, vol. 17, no. 12, pp. 1113-1122, 2001.
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1113-1122
    • Thijs, G.1    Lescot, M.2    Marchal, K.3    Rombauts, S.4    De Moor, B.5    Rouzé, P.6    Moreau, Y.7
  • 48
    • 0036108622 scopus 로고    scopus 로고
    • A Gibbs sampling meyhod to detect over-represented motifs in the upstream regions of co-expressed genes
    • G. Thijs, K. Marchal, M. Lescot, S. Rombauts, B. De Moor, P. Rouzé, and Y. Moreau, "A Gibbs sampling meyhod to detect over-represented motifs in the upstream regions of co-expressed genes," J. Comput. Biol., vol. 9, no. 2, pp. 447-464, 2002.
    • (2002) J. Comput. Biol. , vol.9 , Issue.2 , pp. 447-464
    • Thijs, G.1    Marchal, K.2    Lescot, M.3    Rombauts, S.4    De Moor, B.5    Rouzé, P.6    Moreau, Y.7
  • 50
    • 0033289316 scopus 로고    scopus 로고
    • An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
    • Heidelberg, Germany, Aug.
    • M. Tompa, "An exact method for finding short motifs in sequences, with application to the ribosome binding site problem," in Proc. 7th Intl. Conf. Intelligent Syst. for Mol. Biol., Heidelberg, Germany, Aug. 1999, pp. 262-271.
    • (1999) Proc. 7th Intl. Conf. Intelligent Syst. for Mol. Biol. , pp. 262-271
    • Tompa, M.1
  • 51
    • 0003164597 scopus 로고
    • Pattern classification by distance functions, in
    • Reading, MA: Addison-Wesley
    • J. T. Tou and R. C. Gonzalez, "Pattern classification by distance functions," in Pattern Recognition Principles. Reading, MA: Addison-Wesley, 1979, pp. 75-109.
    • (1979) Pattern Recognition Principles , pp. 75-109
    • Tou, J.T.1    Gonzalez, R.C.2
  • 53
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • J. van Helden, B. André, and L. Collado-Vides, "Extracting regulatory sites from upstream region of yeast genes by computational analysis of oligonucleotide frequencies," J. Mol. Biol., vol. 281, pp. 827-842, 1998.
    • (1998) J. Mol. Biol. , vol.281 , pp. 827-842
    • Van Helden, J.1    André, B.2    Collado-Vides, L.3
  • 54
    • 0034656326 scopus 로고    scopus 로고
    • Discovering regulatory elements in noncoding sequences by analysis of spaced dyads
    • J. van Helden, A. F. Rios, and J. Collado-Vides, "Discovering regulatory elements in noncoding sequences by analysis of spaced dyads," Nucleic Acids Res., vol. 28, no. 8, pp. 1808-1818, 2000.
    • (2000) Nucleic Acids Res. , vol.28 , Issue.8 , pp. 1808-1818
    • Van Helden, J.1    Rios, A.F.2    Collado-Vides, J.3
  • 56
    • 0032776529 scopus 로고    scopus 로고
    • Models for prediction and recognition of éukaryotic promoters
    • T. Werner, "Models for prediction and recognition of éukaryotic promoters," Mammalian Genome, vol. 10, pp. 71-80, 1999.
    • (1999) Mammalian Genome , vol.10 , pp. 71-80
    • Werner, T.1
  • 57
    • 0033655171 scopus 로고    scopus 로고
    • Ann-spec: A method for discovering transcription binding sites with improved specificity
    • Honolulu, HI
    • C. T. Workman and G. D. Stormo, "Ann-spec: A method for discovering transcription binding sites with improved specificity," in Proc. Pacific Symp. Biocomputing, vol. 5, Honolulu, HI, 2000, pp. 464-175.
    • (2000) Proc. Pacific Symp. Biocomputing , vol.5 , pp. 464-1175
    • Workman, C.T.1    Stormo, G.D.2
  • 58
    • 0034782618 scopus 로고    scopus 로고
    • Model-based clustering and data transformations for gene expression data
    • K. Y. Yeung, C. Fraley, A. Murua, A. E. Raftery, and W. L. Ruzzo, "Model-based clustering and data transformations for gene expression data," Bioinformatics, vol. 17, pp. 977-987, 2001.
    • (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
  • 59
    • 0035024021 scopus 로고    scopus 로고
    • Validating clustering for gene expression data
    • K. Y. Yeung, D. R. Haynor, and W. L. Ruzzo, "Validating clustering for gene expression data," Bioinformatics, vol. 17, pp. 309-318, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 309-318
    • Yeung, K.Y.1    Haynor, D.R.2    Ruzzo, W.L.3
  • 60
    • 0034800371 scopus 로고    scopus 로고
    • Principal component analysis for clustering gene expression data
    • K. Y. Yeung and W. L. Ruzzo, "Principal component analysis for clustering gene expression data," Bioinformatics, vol. 17, pp. 763-774, 2001.
    • (2001) Bioinformatics , vol.17 , pp. 763-774
    • Yeung, K.Y.1    Ruzzo, W.L.2
  • 61
    • 0000350651 scopus 로고    scopus 로고
    • Cluster, function and promoter: Analysis of yeast expression array
    • J. Zhu and M. Q. Zhang, "Cluster, function and promoter: Analysis of yeast expression array," in Proc. Pacific Symp. Biocomputing, vol. 5, 2000, pp. 467-486.
    • (2000) Proc. Pacific Symp. Biocomputing , vol.5 , pp. 467-486
    • Zhu, J.1    Zhang, M.Q.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.