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Volumn 23, Issue 10, 2007, Pages 1225-1234

Domain-enhanced analysis of microarray data using GO annotations

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE GRANULOCYTIC LEUKEMIA; ACUTE LYMPHOBLASTIC LEUKEMIA; ANALYTIC METHOD; ARTICLE; B CELL LEUKEMIA; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DOMAIN ENHANCED ANALYSIS; FISHER EXACT TEST; GENE EXPRESSION PROFILING; GENETIC ALGORITHM; HUMAN; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; PRIORITY JOURNAL; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; SIGNAL TRANSDUCTION; SIMULATION; T CELL LEUKEMIA;

EID: 34447331011     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm092     Document Type: Article
Times cited : (18)

References (43)
  • 1
    • 1542399989 scopus 로고    scopus 로고
    • Fatigo: A web tool for finding significant association of gene ontology terms with groups of genes
    • Al-Shahrour,F. et al. (2003) Fatigo: A web tool for finding significant association of gene ontology terms with groups of genes. Bioinformatics, 20, 578-580.
    • (2003) Bioinformatics , vol.20 , pp. 578-580
    • Al-Shahrour, F.1
  • 2
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating go graph structure
    • Alexa,A. et al. (2006) Improved scoring of functional groups from gene expression data by decorrelating go graph structure. Bioinformatics, 22, 1600-1607.
    • (2006) Bioinformatics , vol.22 , pp. 1600-1607
    • Alexa, A.1
  • 3
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology
    • Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 4
    • 18744389489 scopus 로고    scopus 로고
    • Significance analysis of functional categories in gene expression studies: A structured permutation approach
    • Barry,W.T. et al. (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
  • 5
    • 10144260674 scopus 로고    scopus 로고
    • Pls generalised linear regression
    • Bastien,P. et al. (2005) Pls generalised linear regression. Comput. Stat. Data Anal., 48, 17-46.
    • (2005) Comput. Stat. Data Anal , vol.48 , pp. 17-46
    • Bastien, P.1
  • 6
    • 3142665525 scopus 로고    scopus 로고
    • Gostat: Findstatistically overrepresented gene ontologies within a group of genes
    • Beissbarth,T. and Speed,T.P. (2004) Gostat: Findstatistically overrepresented gene ontologies within a group of genes. Bioinformatics, 20, 1464-1465.
    • (2004) Bioinformatics , vol.20 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.P.2
  • 7
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini,Y. and Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc., B, 57, 289-300.
    • (1995) J. R. Stat. Soc., B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 8
    • 0347513219 scopus 로고    scopus 로고
    • Characterizing gene sets with funcassociate
    • Berriz,G.F. et al. (2003) Characterizing gene sets with funcassociate. Bioinformatics, 19, 2502-2504.
    • (2003) Bioinformatics , vol.19 , pp. 2502-2504
    • Berriz, G.F.1
  • 9
    • 0038522873 scopus 로고    scopus 로고
    • Genemerge-post-genomic analysis, data mining, and hypothesis testing
    • Castillo-Davis,C. and Hartl,D.L. (2003) Genemerge-post-genomic analysis, data mining, and hypothesis testing. Bioinformatics, 19, 891-892.
    • (2003) Bioinformatics , vol.19 , pp. 891-892
    • Castillo-Davis, C.1    Hartl, D.L.2
  • 10
    • 1642317557 scopus 로고    scopus 로고
    • Gene expression profile of adult t-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival
    • Chiaretti,S. et al. (2004) Gene expression profile of adult t-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival. Blood, 103, 2771-2778.
    • (2004) Blood , vol.103 , pp. 2771-2778
    • Chiaretti, S.1
  • 11
    • 0036578644 scopus 로고    scopus 로고
    • Genemapp, a new tool for viewing and analyzing microarray data on biological pathways
    • Dahlquist,K.D. et al. (2002) Genemapp, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet., 31, 19-20.
    • (2002) Nat. Genet , vol.31 , pp. 19-20
    • Dahlquist, K.D.1
  • 13
    • 0027530250 scopus 로고
    • Simpls: An alternative approach to partial least squares regression
    • de Jong,S. (1993) Simpls: An alternative approach to partial least squares regression. Chemom. Intell. Lab Syst., 18: 251-263.
    • (1993) Chemom. Intell. Lab Syst , vol.18 , pp. 251-263
    • de Jong, S.1
  • 14
    • 20744452472 scopus 로고    scopus 로고
    • Classification using generalized partial least squares
    • Ding,B. and Gentleman,R. (2005) Classification using generalized partial least squares. J. Comput. Graph. Stat., 14, 280-298.
    • (2005) J. Comput. Graph. Stat , vol.14 , pp. 280-298
    • Ding, B.1    Gentleman, R.2
  • 15
    • 0037293075 scopus 로고    scopus 로고
    • Global functional profiling of gene expression
    • Draghici,S. et al. (2003a) Global functional profiling of gene expression. Genomics, 81, 98-104.
    • (2003) Genomics , vol.81 , pp. 98-104
    • Draghici, S.1
  • 16
    • 0042121055 scopus 로고    scopus 로고
    • Onto-tools, the toolkit of the modern biologist: Onto-express, onto-compare, onto-design and onto-translate
    • Draghici,S. et al. (2003b) Onto-tools, the toolkit of the modern biologist: Onto-express, onto-compare, onto-design and onto-translate. Nucleic Acids Res., 31, 3775-3781.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3775-3781
    • Draghici, S.1
  • 17
    • 1542784653 scopus 로고    scopus 로고
    • Empirical bayes analysis of a microarray experiment
    • Efron,B. et al. (2001) Empirical bayes analysis of a microarray experiment. J. Am. Stat. Assoc., 96, 1151-1160.
    • (2001) J. Am. Stat. Assoc , vol.96 , pp. 1151-1160
    • Efron, B.1
  • 18
    • 16344365619 scopus 로고    scopus 로고
    • Classification using partial least squares with penalized logistic regression
    • Fort,G. and Lambert-Lacroix,S. (2005) Classification using partial least squares with penalized logistic regression. Bioinformatics, 21 1104-1111.
    • (2005) Bioinformatics , vol.21 , pp. 1104-1111
    • Fort, G.1    Lambert-Lacroix, S.2
  • 19
    • 0345832338 scopus 로고    scopus 로고
    • A global test for groups of genes: Testing association with a clinical outcome
    • Goeman,J. 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.1
  • 20
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
    • Golub,T.R. 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
  • 21
    • 85162676194 scopus 로고
    • Pls regression methods
    • Hoskuldson,A. (1988) Pls regression methods. J. Chemom., 2, 211-228.
    • (1988) J. Chemom , vol.2 , pp. 211-228
    • Hoskuldson, A.1
  • 22
    • 0242559063 scopus 로고    scopus 로고
    • Linear regression and two-class classification with gene expression data
    • Huang,X. and Pan,W. (2003) Linear regression and two-class classification with gene expression data. Bioinformatics, 19 2072-2078.
    • (2003) Bioinformatics , vol.19 , pp. 2072-2078
    • Huang, X.1    Pan, W.2
  • 23
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: Current tools, limitations, and open problems
    • Khatri,P. and 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
  • 24
    • 25444502609 scopus 로고    scopus 로고
    • Page: Parametric analysis of gene set enrichment
    • Kim,S.-Y. and 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
  • 25
    • 27944474776 scopus 로고    scopus 로고
    • Erminej: Tool for functional analysis of gene expression data sets
    • Lee,H. et al. (2005) Erminej: Tool for functional analysis of gene expression data sets. BMC Bioinformatics, 6, 269.
    • (2005) BMC Bioinformatics , vol.6 , pp. 269
    • Lee, H.1
  • 26
    • 12344271032 scopus 로고    scopus 로고
    • Dimension reduction methods for microarrays with application to censored survival data
    • Li,L. and Li,H. (2004) Dimension reduction methods for microarrays with application to censored survival data. Bioinformatics, 20, 3406-3412.
    • (2004) Bioinformatics , vol.20 , pp. 3406-3412
    • Li, L.1    Li, H.2
  • 28
    • 0030703030 scopus 로고    scopus 로고
    • Nonlinear partial least squares
    • Malthouse,E. et al. (1997) Nonlinear partial least squares. Comput. Chem. Eng., 21, 875-890.
    • (1997) Comput. Chem. Eng , vol.21 , pp. 875-890
    • Malthouse, E.1
  • 29
    • 0034352940 scopus 로고    scopus 로고
    • Power sage: Comparing statistical tests for sage experiments
    • Man,M.Z. et al. (2000) Power sage: Comparing statistical tests for sage experiments. Bioinformatics, 16, 953-955.
    • (2000) Bioinformatics , vol.16 , pp. 953-955
    • Man, M.Z.1
  • 30
    • 0242718698 scopus 로고    scopus 로고
    • Iteratively reweighted partial least squares estimation for generalized linear regression
    • Marx,B. (1996) Iteratively reweighted partial least squares estimation for generalized linear regression. Technometrics, 38, 374-381.
    • (1996) Technometrics , vol.38 , pp. 374-381
    • Marx, B.1
  • 31
    • 0038054341 scopus 로고    scopus 로고
    • Pgc-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha,V. et al. (2003) Pgc-1α-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.1
  • 32
    • 33748690756 scopus 로고    scopus 로고
    • Adgo: Analysis of differentially expressed gene sets using composite go annotation
    • Nam,D. et al. (2006) Adgo: Analysis of differentially expressed gene sets using composite go annotation. Bioinformatics, 22, 2249-2253.
    • (2006) Bioinformatics , vol.22 , pp. 2249-2253
    • Nam, D.1
  • 33
    • 0036740519 scopus 로고    scopus 로고
    • Multi-class cancer classification via partial least squares with gene expression profiles
    • Nguyen,D.V. and Rocke,D.M. (2002a) Multi-class cancer classification via partial least squares with gene expression profiles. Bioinformatics 18, 1216-1226.
    • (2002) Bioinformatics , vol.18 , pp. 1216-1226
    • Nguyen, D.V.1    Rocke, D.M.2
  • 34
    • 0036166439 scopus 로고    scopus 로고
    • Tumor classification by partial least squares using microarray gene expression data
    • Nguyen,D.V. and Rocke.,D.M. (2002b) Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 18, 39-50.
    • (2002) Bioinformatics , vol.18 , pp. 39-50
    • Nguyen, D.V.1    Rocke, D.M.2
  • 35
    • 2642537531 scopus 로고    scopus 로고
    • On partial least squares dimentsion reduction from microarray-based classification: A simulation study
    • Nguyen,D.V. and Rocke.,D.M. (2004) On partial least squares dimentsion reduction from microarray-based classification: A simulation study. Comput. Stat. Data Anal., 46, 407-425.
    • (2004) Comput. Stat. Data Anal , vol.46 , pp. 407-425
    • Nguyen, D.V.1    Rocke, D.M.2
  • 37
    • 0006048396 scopus 로고    scopus 로고
    • A mixture model approach to detecting differentially expressed genes with microarray data
    • 2001-011. Division of Biostatistics, University of Minnesota
    • Pan,W. et al. (2001) A mixture model approach to detecting differentially expressed genes with microarray data. Research Report 2001-011. Division of Biostatistics, University of Minnesota.
    • (2001) Research Report
    • Pan, W.1
  • 38
    • 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
  • 39
    • 26444608611 scopus 로고    scopus 로고
    • Discovering statistically significant pathways in expression profiling studies
    • Tian,L. et al. (2005) Discovering statistically significant pathways in expression profiling studies. Proc. Natl Acad. Sci. USA 102, 13544-13549.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13544-13549
    • Tian, L.1
  • 40
    • 0035942271 scopus 로고    scopus 로고
    • Signficance analysis of microarrays applied to the ionizing radiation response
    • Tusher,V.G. et al. (2001) Signficance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5121.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 5116-5121
    • Tusher, V.G.1
  • 41
    • 0027943145 scopus 로고
    • Comparing the predictive accuracy of models using a simple randomization test
    • van der Voet,H. (1994) Comparing the predictive accuracy of models using a simple randomization test. Chemom Intell Lab Syst., 25, 313-323.
    • (1994) Chemom Intell Lab Syst , vol.25 , pp. 313-323
    • van der Voet, H.1
  • 42
    • 0038175144 scopus 로고    scopus 로고
    • Gominer: A resource for biological interpretation of genomic and proteomic data
    • Zeeberg,B.R. et al. (2003) Gominer: A resource for biological interpretation of genomic and proteomic data. Bioinformatics, 4 R28.
    • (2003) Bioinformatics , vol.4
    • Zeeberg, B.R.1
  • 43
    • 0042121250 scopus 로고    scopus 로고
    • Chipinfo: Software for extracting gene annotation and gene ontology information for microarray analysis
    • Zhong,S. et al. (2003) Chipinfo: Software for extracting gene annotation and gene ontology information for microarray analysis. Nucleic Acids Res., 31, 3483-3486.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3483-3486
    • Zhong, S.1


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