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Volumn 453, Issue , 2008, Pages 245-255

Expression and microarrays

Author keywords

Functional genomics; Functional interpretation; Gene ontology; Multiple testing

Indexed keywords


EID: 84934439869     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-429-6_12     Document Type: Article
Times cited : (1)

References (44)
  • 1
    • 25144498379 scopus 로고    scopus 로고
    • A human protein-protein interaction network: A resource for annotating the proteome
    • Stelzl, U., Worm, U., Lalowski, M., Haenig, C., et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122, 957-968.
    • (2005) Cell , vol.122 , pp. 957-968
    • Stelzl, U.1    Worm, U.2    Lalowski, M.3    Haenig, C.4
  • 2
    • 30344439849 scopus 로고    scopus 로고
    • Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity
    • Hallikas, O., Palin, K., Sinjushina, N., et al. (2006) Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, 47-59.
    • (2006) Cell , vol.124 , pp. 47-59
    • Hallikas, O.1    Palin, K.2    Sinjushina, N.3
  • 3
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteome-scale map of the human protein-protein interaction network
    • Rual, J. F., Venkatesan, K., Hao, T., et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437, 1173-1178.
    • (2005) Nature , vol.437 , pp. 1173-1178
    • Rual, J.F.1    Venkatesan, K.2    Hao, T.3
  • 4
    • 3042514191 scopus 로고    scopus 로고
    • Coexpression analysis of human genes across many microarray data sets
    • Lee, H. K., Hsu, A. K., Sajdak, J., et al. (2004) Coexpression analysis of human genes across many microarray data sets. Genome Res 14, 1085-1094.
    • (2004) Genome Res , vol.14 , pp. 1085-1094
    • Lee, H.K.1    Hsu, A.K.2    Sajdak, J.3
  • 5
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart, J. M., Segal, E., Koller, D., et al. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-255.
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3
  • 6
    • 0037407924 scopus 로고    scopus 로고
    • Predicting gene function by conserved co-expression
    • van Noort, V., Snel, B., Huynen, M. A. (2003) Predicting gene function by conserved co-expression. Trends Genet 19, 238-242.
    • (2003) Trends Genet , vol.19 , pp. 238-242
    • van Noort, V.1    Snel, B.2    Huynen, M.A.3
  • 7
    • 0036852181 scopus 로고    scopus 로고
    • Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons
    • Mateos, A., Dopazo, J., Jansen, R., et al. (2002) Systematic learning of gene functional classes from DNA array expression data by using multilayer perceptrons. Genome Res 12, 1703-1715.
    • (2002) Genome Res , vol.12 , pp. 1703-1715
    • Mateos, A.1    Dopazo, J.2    Jansen, R.3
  • 8
    • 5044227742 scopus 로고    scopus 로고
    • The evolution of molecular biology into systems biology
    • Westerhoff, H. V., Palsson, B. O. (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22, 1249-1252.
    • (2004) Nat Biotechnol , vol.22 , pp. 1249-1252
    • Westerhoff, H.V.1    Palsson, B.O.2
  • 9
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
    • Golub, T. R., Slonim, D. K., Tamayo, P., et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531-537.
    • (1999) Science , vol.286 , pp. 531-537
    • Golub, T.R.1    Slonim, D.K.2    Tamayo, P.3
  • 10
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M., Ball, C. A., Blake, J. A., 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    Ball, C.A.2    Blake, J.A.3
  • 11
    • 0345863935 scopus 로고    scopus 로고
    • The KEGG resource for deciphering the genome
    • Kanehisa, M., Goto, S., Kawashima, S., et al. (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32, D277-280.
    • (2004) Nucleic Acids Res , vol.32
    • Kanehisa, M.1    Goto, S.2    Kawashima, S.3
  • 12
    • 33644859558 scopus 로고    scopus 로고
    • cisRED: A database system for genome-scale computational discovery of regulatory elements
    • Robertson, G., Bilenky, M., Lin, K., et al. (2006) cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res 34, D68-73.
    • (2006) Nucleic Acids Res , vol.34
    • Robertson, G.1    Bilenky, M.2    Lin, K.3
  • 13
    • 0033976586 scopus 로고    scopus 로고
    • TRANSFAC: An integrated system for gene expression regulation
    • Wingender, E., Chen, X., Hehl, R., et al. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res 28, 316-319.
    • (2000) Nucleic Acids Res , vol.28 , pp. 316-319
    • Wingender, E.1    Chen, X.2    Hehl, R.3
  • 15
    • 0037293075 scopus 로고    scopus 로고
    • Global functional profiling of gene expression
    • Draghici, S., Khatri, P., Martins, R. P., et al. (2003) Global functional profiling of gene expression. Genomics 81, 98-104.
    • (2003) Genomics , vol.81 , pp. 98-104
    • Draghici, S.1    Khatri, P.2    Martins, R.P.3
  • 16
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
    • Al-Shahrour, F., Diaz-Uriarte, R., Dopazo, J. (2004) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20, 578-580.
    • (2004) Bioinformatics , vol.20 , pp. 578-580
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 17
    • 0038175144 scopus 로고    scopus 로고
    • GoMiner: A resource for biological interpretation of genomic and proteomic data
    • Zeeberg, B. R., Feng, W., Wang, G., et al. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4, R28.
    • (2003) Genome Biol , vol.4
    • Zeeberg, B.R.1    Feng, W.2    Wang, G.3
  • 18
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: Current tools, limitations, and open problems
    • Khatri, P., Draghici, S. (2005) Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21, 3587-3595.
    • (2005) Bioinformatics , vol.21 , pp. 3587-3595
    • Khatri, P.1    Draghici, S.2
  • 19
    • 19544366640 scopus 로고    scopus 로고
    • A knowledge-driven approach to cluster validity assessment
    • Bolshakova, N., Azuaje, F., Cunningham, P. (2005) A knowledge-driven approach to cluster validity assessment. Bioinformatics 21, 2546-2547.
    • (2005) Bioinformatics , vol.21 , pp. 2546-2547
    • Bolshakova, N.1    Azuaje, F.2    Cunningham, P.3
  • 20
    • 18244389201 scopus 로고    scopus 로고
    • Standardizing global gene expression analysis between laboratories and across platforms
    • Bammler, T., Beyer, R. P., Bhattacharya, S., et al. (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2, 351-356.
    • (2005) Nat Methods , vol.2 , pp. 351-356
    • Bammler, T.1    Beyer, R.P.2    Bhattacharya, S.3
  • 21
    • 0038054341 scopus 로고    scopus 로고
    • PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha, V. K., Lindgren, C. M., Eriksson, K. F., et al. (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34, 267-273.
    • (2003) Nat Genet , vol.34 , pp. 267-273
    • Mootha, V.K.1    Lindgren, C.M.2    Eriksson, K.F.3
  • 22
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A., Tamayo, P., Mootha, V. K., et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102, 15545-15550.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3
  • 23
    • 3042745465 scopus 로고    scopus 로고
    • Statistical concerns about the GSEA procedure
    • Damian, D., Gorfine, M. (2004) Statistical concerns about the GSEA procedure. Nat Genet 36, 663.
    • (2004) Nat Genet , vol.36 , pp. 663
    • Damian, D.1    Gorfine, M.2
  • 24
    • 21444442035 scopus 로고    scopus 로고
    • Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information
    • Al-Shahrour, F., Diaz-Uriarte, R., Dopazo, J. (2005) Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information. Bioinformatics 21, 2988-2993.
    • (2005) Bioinformatics , vol.21 , pp. 2988-2993
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 25
    • 18744406044 scopus 로고    scopus 로고
    • Testing association of a pathway with survival using gene expression data
    • Goeman, J. J., Oosting, J., Cleton-Jansen, A. M., et al. (2005) Testing association of a pathway with survival using gene expression data. Bioinformatics 21, 1950-1957.
    • (2005) Bioinformatics , vol.21 , pp. 1950-1957
    • Goeman, J.J.1    Oosting, J.2    Cleton-Jansen, A.M.3
  • 26
    • 0345832338 scopus 로고    scopus 로고
    • A global test for groups of genes: Testing association with a clinical outcome
    • Goeman, J. J., van de Geer, S. A., de Kort, F., et al. (2004) A global test for groups of genes: testing association with a clinical outcome. Bioinformatics, 20, 93-99.
    • (2004) Bioinformatics , vol.20 , pp. 93-99
    • Goeman, J.J.1    van de Geer, S.A.2    de Kort, F.3
  • 27
    • 26444608611 scopus 로고    scopus 로고
    • Discovering statistically significant pathways in expression profiling studies
    • Tian, L., Greenberg, S. A., Kong, S. W., et al. (2005) Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci U S A 102, 13544-13549.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 13544-13549
    • Tian, L.1    Greenberg, S.A.2    Kong, S.W.3
  • 28
    • 8844265260 scopus 로고    scopus 로고
    • GO-Mapper: Functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
    • Smid, M., Dorssers, L. C. (2004) GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms. Bioinformatics 20, 2618-2625.
    • (2004) Bioinformatics , vol.20 , pp. 2618-2625
    • Smid, M.1    Dorssers, L.C.2
  • 29
    • 33645851033 scopus 로고    scopus 로고
    • BayGO: Bayesian analysis of ontology term enrichment in microarray data
    • Vencio, R., Koide, T., Gomes, S., et al. (2006) BayGO: Bayesian analysis of ontology term enrichment in microarray data. BMC Bioinformatics 7, 86.
    • (2006) BMC Bioinformatics , vol.7 , pp. 86
    • Vencio, R.1    Koide, T.2    Gomes, S.3
  • 30
    • 25444502609 scopus 로고    scopus 로고
    • PAGE: Parametric analysis of gene set enrichment
    • Kim, S. Y., Volsky, D. J. (2005) PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 6, 144.
    • (2005) BMC Bioinformatics , vol.6 , pp. 144
    • Kim, S.Y.1    Volsky, D.J.2
  • 31
    • 33644779837 scopus 로고    scopus 로고
    • GO-Diff: Mining functional differentiation between EST-based transcriptomes
    • Chen, Z., Wang, W., Ling, X. B., et al. (2006) GO-Diff: Mining functional differentiation between EST-based transcriptomes. BMC Bioinformatics 7, 72.
    • (2006) BMC Bioinformatics , vol.7 , pp. 72
    • Chen, Z.1    Wang, W.2    Ling, X.B.3
  • 32
    • 33747859675 scopus 로고    scopus 로고
    • BABELOMICS: A systems biology perspective in the functional annotation of genome-scale experiments
    • Al-Shahrour, F., Minguez, P., Tarraga, J., et al. (2006) BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res 34, W472-476.
    • (2006) Nucleic Acids Res , vol.34
    • Al-Shahrour, F.1    Minguez, P.2    Tarraga, J.3
  • 33
    • 21444445084 scopus 로고    scopus 로고
    • BABELOMICS: A suite of web tools for functional annotation and Expression and Microarrays 255 analysis of groups of genes in high-throughput experiments
    • Al-Shahrour, F., Minguez, P., Vaquerizas, J. M., et al. (2005) BABELOMICS: a suite of web tools for functional annotation and Expression and Microarrays 255 analysis of groups of genes in high-throughput experiments. Nucleic Acids Res, 33, W460-464.
    • (2005) Nucleic Acids Res , vol.33
    • Al-Shahrour, F.1    Minguez, P.2    Vaquerizas, J.M.3
  • 34
    • 33646895693 scopus 로고    scopus 로고
    • Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data
    • Huang, D., Pan, W. (2006) Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data. Bioinformatics 22, 1259-1268.
    • (2006) Bioinformatics , vol.22 , pp. 1259-1268
    • Huang, D.1    Pan, W.2
  • 35
    • 33645289673 scopus 로고    scopus 로고
    • Incorporating gene functions as priors in model-based clustering of microarray gene expression data
    • Pan, W. (2006) Incorporating gene functions as priors in model-based clustering of microarray gene expression data. Bioinformatics 22, 795-801.
    • (2006) Bioinformatics , vol.22 , pp. 795-801
    • Pan, W.1
  • 36
    • 31744434873 scopus 로고    scopus 로고
    • Clustering expressed genes on the basis of their association with a quantitative phenotype
    • Jia, Z., Xu, S. (2005) Clustering expressed genes on the basis of their association with a quantitative phenotype. Genet Res 86, 193-207.
    • (2005) Genet Res , vol.86 , pp. 193-207
    • Jia, Z.1    Xu, S.2
  • 37
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen, M. B., Spellman, P. T., Brown, P. O., et al. (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95, 14863-14868.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 14863-14868
    • Eisen, M.B.1    Spellman, P.T.2    Brown, P.O.3
  • 38
    • 25444476441 scopus 로고    scopus 로고
    • Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
    • Wolfe, C.J., Kohane, I. S., and Butte, A. J. (2005) Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks. BMC Bioinformatics 6, 227.
    • (2005) BMC Bioinformatics , vol.6 , pp. 227
    • Wolfe, C.J.1    Kohane, I.S.2    Butte, A.J.3
  • 39
    • 18744389489 scopus 로고    scopus 로고
    • Significance analysis of functional categories in gene expression studies: A structured permutation approach
    • Barry, W. T., Nobel, A. B., and Wright, F. A. (2005) Significance analysis of functional categories in gene expression studies: a structured permutation approach. Bioinformatics 21, 1943-1949.
    • (2005) Bioinformatics , vol.21 , pp. 1943-1949
    • Barry, W.T.1    Nobel, A.B.2    Wright, F.A.3
  • 40
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Benjamini, Y., Yekutieli, D. (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29, 1165-1188.
    • (2001) Ann Stat , vol.29 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 41
    • 0042121252 scopus 로고    scopus 로고
    • GEPAS: A web-based resource for microarray gene expression data analysis
    • Herrero, J., Al-Shahrour, F., Diaz-Uriarte, R., et al. (2003) GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res 31, 3461-3467.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3461-3467
    • Herrero, J.1    Al-Shahrour, F.2    Diaz-Uriarte, R.3
  • 42
    • 3242882895 scopus 로고    scopus 로고
    • New challenges in gene expression data analysis and the extended GEPAS
    • Herrero, J., Vaquerizas, J. M., Al-Shahrour, F., et al. (2004) New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res 32, W485-491.
    • (2004) Nucleic Acids Res , vol.32
    • Herrero, J.1    Vaquerizas, J.M.2    Al-Shahrour, F.3
  • 43
    • 23144439117 scopus 로고    scopus 로고
    • GEPAS, an experimentoriented pipeline for the analysis of microarray gene expression data
    • Vaquerizas, J. M., Conde, L., Yankilevich, P., et al. (2005) GEPAS, an experimentoriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res 33, W616-620.
    • (2005) Nucleic Acids Res , vol.33
    • Vaquerizas, J.M.1    Conde, L.2    Yankilevich, P.3
  • 44
    • 18744414232 scopus 로고    scopus 로고
    • Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data
    • Lottaz, C., Spang, R. (2005) Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. Bioinformatics 21, 1971-1978.
    • (2005) Bioinformatics , vol.21 , pp. 1971-1978
    • Lottaz, C.1    Spang, R.2


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