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Volumn 41, Issue 7, 2013, Pages

Ensuring the statistical soundness of competitive gene set approaches: Gene filtering and genome-scale coverage are essential

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[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 84876544061     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt054     Document Type: Article
Times cited : (22)

References (41)
  • 1
    • 37049235151 scopus 로고
    • The theory of open systems in physics and biology
    • von Bertalanffy, L. (1950) The theory of open systems in physics and biology. Science, 111, 23-29.
    • (1950) Science , vol.111 , pp. 23-29
    • Von Bertalanffy, L.1
  • 2
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • DOI 10.1038/nrg1272
    • Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat. Rev., 5, 101-113. (Pubitemid 38160277)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.2 , pp. 101-113
    • Barabasi, A.-L.1    Oltvai, Z.N.2
  • 3
    • 79960325408 scopus 로고    scopus 로고
    • Networks for systems biology: Conceptual connection of data and function
    • Emmert-Streib, F. and Dehmer, M. (2011) Networks for systems biology: conceptual connection of data and function. IET Syst. Biol., 5, 185-207.
    • (2011) IET Syst. Biol , vol.5 , pp. 185-207
    • Emmert-Streib, F.1    Dehmer, M.2
  • 5
    • 33751361595 scopus 로고    scopus 로고
    • Cambridge University Press, Cambridge; New York
    • Palsson, B. (2006) Systems Biology. Cambridge University Press, Cambridge; New York.
    • (2006) Systems Biology
    • Palsson, B.1
  • 6
    • 71349087490 scopus 로고    scopus 로고
    • A unifying view of 21st century systems biology
    • Vidal, M. (2009) A unifying view of 21st century systems biology. FEBS Lett., 583, 3891-3894.
    • (2009) FEBS Lett , vol.583 , pp. 3891-3894
    • Vidal, M.1
  • 7
    • 67349276056 scopus 로고    scopus 로고
    • A network medicine approach to human disease
    • Zanzoni, A., Soler-Lopez, M. and Aloy, P. (2009) A network medicine approach to human disease. FEBS Lett., 583, 1759-1765.
    • (2009) FEBS Lett , vol.583 , pp. 1759-1765
    • Zanzoni, A.1    Soler-Lopez, M.2    Aloy, P.3
  • 9
    • 79958152651 scopus 로고    scopus 로고
    • Pathway analysis of expression data: Deciphering functional building blocks of complex diseases
    • Emmert-Streib, F. and Glazko, G. (2011) Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput. Biol., 7, e1002053.
    • (2011) PLoS Comput. Biol , vol.7
    • Emmert-Streib, F.1    Glazko, G.2
  • 12
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M. and Goto, S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nuclei Acids Res., 28, 27-30. (Pubitemid 30047706)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 14
    • 34548747580 scopus 로고    scopus 로고
    • The chronic fatigue syndrome: A comparative pathway analysis
    • DOI 10.1089/cmb.2007.0041
    • Emmert-Streib, F. (2007) The chronic fatigue syndrome: a comparative pathway analysis. J. Comput. Biol., 14, 961-972. (Pubitemid 47427602)
    • (2007) Journal of Computational Biology , vol.14 , Issue.7 , pp. 961-972
    • Emmert-Streib, F.1
  • 15
    • 69849105388 scopus 로고    scopus 로고
    • Unite and conquer: Univariate and multivariate approaches for finding differentially expressed gene sets
    • Glazko, G. and Emmert-Streib, F. (2009) Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets. Bioinformatics, 25, 2348-2354.
    • (2009) Bioinformatics , vol.25 , pp. 2348-2354
    • Glazko, G.1    Emmert-Streib, F.2
  • 17
    • 79955766601 scopus 로고    scopus 로고
    • Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes
    • Jung, K., Becker, B., Brunner, E. and Beiarth, T. (2011) Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes. Bioinformatics, 27, 1377-1383.
    • (2011) Bioinformatics , vol.27 , pp. 1377-1383
    • Jung, K.1    Becker, B.2    Brunner, E.3    Beiarth, T.4
  • 19
    • 43149116763 scopus 로고    scopus 로고
    • Gene-set approach for expression pattern analysis
    • DOI 10.1093/bib/bbn001
    • Nam, D. and Kim, S. (2008) Gene-set approach for expression pattern analysis. Brief Bioinform., 9, 189-197. (Pubitemid 351637941)
    • (2008) Briefings in Bioinformatics , vol.9 , Issue.3 , pp. 189-197
    • Nam, D.1    Kim, S.-Y.2
  • 20
    • 63449107173 scopus 로고    scopus 로고
    • A general modular framework for gene set enrichment analysis
    • Ackermann, M. and Strimmer, K. (2009) A general modular framework for gene set enrichment analysis. BMC Bioinformatics, 10, 47.
    • (2009) BMC Bioinformatics , vol.10 , pp. 47
    • Ackermann, M.1    Strimmer, K.2
  • 21
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: Methodological issues
    • DOI 10.1093/bioinformatics/btm051
    • Goeman, J. and Buhlmann, P. (2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics, 23, 980-987. (Pubitemid 47050585)
    • (2007) Bioinformatics , vol.23 , Issue.8 , pp. 980-987
    • Goeman, J.J.1    Buhlmann, P.2
  • 22
    • 84869590034 scopus 로고    scopus 로고
    • Rotation testing in gene set enrichment analysis for small direct comparison experiments
    • SS. Article 34
    • Dum, G., Snipen, L., Solheim, M. and SS. (2009) Rotation testing in gene set enrichment analysis for small direct comparison experiments. Stat. Appl. Genet. Mol. Biol., 8, Article 34.
    • (2009) Stat. Appl. Genet. Mol. Biol , vol.8
    • Dum, G.1    Snipen, L.2    Solheim, M.3
  • 23
    • 34250305651 scopus 로고    scopus 로고
    • Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis
    • Newton, M., Quintana, F., denBoon, J.A., Sengupta, S. and Ahlquist, P. (2007) Random-set methods identify distinct aspects of the enrichment signal in gene-set analysis. Ann. Appl. Stat., 1, 85-106.
    • (2007) Ann. Appl. Stat , vol.1 , pp. 85-106
    • Newton, M.1    Quintana, F.2    Denboon, J.A.3    Sengupta, S.4    Ahlquist, P.5
  • 25
    • 35348890683 scopus 로고    scopus 로고
    • On testing the significance of sets of genes
    • Efron, B. and Tibshiran, R. (2007) On testing the significance of sets of genes. Ann. Appl. Stat., 1, 107-129.
    • (2007) Ann. Appl. Stat , vol.1 , pp. 107-129
    • Efron, B.1    Tibshiran, R.2
  • 29
    • 77956524952 scopus 로고    scopus 로고
    • De-correlating expression in gene-set analysis
    • Nam, D. (2010) De-correlating expression in gene-set analysis. Bioinformatics, 26, i511-i516.
    • (2010) Bioinformatics , vol.26
    • Nam, D.1
  • 30
    • 27144468989 scopus 로고    scopus 로고
    • Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation
    • DOI 10.1158/1078-0432.CCR-04-2165
    • Chiaretti, S., Li, X., Gentleman, R., Vitale, A., Wang, K.S., Mandelli, F., Foa, R. and Ritz, J. (2005) Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation. Clin. Cancer Res., 11, 7209-7219. (Pubitemid 41507677)
    • (2005) Clinical Cancer Research , vol.11 , Issue.20 , pp. 7209-7219
    • Chiaretti, S.1    Li, X.2    Gentleman, R.3    Vitale, A.4    Wang, K.S.5    Mandelli, F.6    Foa, R.7    Ritz, J.8
  • 33
    • 77953095629 scopus 로고    scopus 로고
    • Independent filtering increases detection power for high-throughput experiments
    • Bourgon, R., Gentleman, R. and Huber, W. (2010) Independent filtering increases detection power for high-throughput experiments. Proc. Natl Acad. Sci. USA, 107, 9546-9551.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 9546-9551
    • Bourgon, R.1    Gentleman, R.2    Huber, W.3
  • 34
    • 31444431754 scopus 로고    scopus 로고
    • Reliability and reproducibility issues in DNA microarray measurements
    • DOI 10.1016/j.tig.2005.12.005, PII S0168952505003598
    • Draghici, S., Khatri, P., Eklund, A.C. and Szallasi, Z. (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet., 22, 101-109. (Pubitemid 43152029)
    • (2006) Trends in Genetics , vol.22 , Issue.2 , pp. 101-109
    • Draghici, S.1    Khatri, P.2    Eklund, A.C.3    Szallasi, Z.4
  • 35
    • 77953916879 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. Ser. B (Methodological), 57, 125-133.
    • (1995) J. R. Stat. Soc. Ser. B (Methodological) , vol.57 , pp. 125-133
    • Benjamini, Y.1    Hochberg, Y.2
  • 37
    • 75649135574 scopus 로고    scopus 로고
    • RNA-seq: From technology to biology
    • Marguerat, S. and Bahler, J. (2010) RNA-seq: from technology to biology. Cell. Mol. Life Sci., 67, 569-579.
    • (2010) Cell. Mol. Life Sci , vol.67 , pp. 569-579
    • Marguerat, S.1    Bahler, J.2
  • 38
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 39
    • 84876564367 scopus 로고    scopus 로고
    • GSEA team GSEA User Guide v3.82 The Broad Institute Boston USA 2011
    • GSEA team GSEA User Guide v3.82 The Broad Institute Boston, USA. (2011) http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html.
  • 41
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
    • Huang, D.W., Sherman, B.T. and Lempicki, R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
    • (2009) Nucleic Acids Res , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3


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