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Volumn 26, Issue 20, 2010, Pages 2586-2593

Module-based prediction approach for robust inter-study predictions in microarray data

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGY; CLUSTER ANALYSIS; DNA MICROARRAY; FACTUAL DATABASE; GENE EXPRESSION PROFILING; METHODOLOGY;

EID: 77957786147     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq472     Document Type: Article
Times cited : (8)

References (49)
  • 1
    • 18544365698 scopus 로고    scopus 로고
    • Gene-expression profiles predict survival of patients with lung adenocarcinoma
    • Beer,D.G. et al. (2002) Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat. Med., 8, 816-824.
    • (2002) Nat. Med. , vol.8 , pp. 816-824
    • Beer, D.G.1
  • 2
    • 33644813589 scopus 로고    scopus 로고
    • Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories
    • Bhanot,G. et al. (2005) Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories. Genome Inform., 16, 233-244.
    • (2005) Genome Inform. , vol.16 , pp. 233-244
    • Bhanot, G.1
  • 3
    • 0035923521 scopus 로고    scopus 로고
    • Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses
    • Bhattacharjee,A. et al. (2001) Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses. Proc. Natl Acad. Sci. USA, 98, 13790-13795.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 13790-13795
    • Bhattacharjee, A.1
  • 4
    • 1542574379 scopus 로고    scopus 로고
    • Multi-platform, multi-site, microarray-based human tumor classification
    • Bloom,G. et al. (2004) Multi-platform, multi-site, microarray-based human tumor classification. Am. J. Pathol., 164, 9-16.
    • (2004) Am. J. Pathol. , vol.164 , pp. 9-16
    • Bloom, G.1
  • 5
    • 34248183381 scopus 로고    scopus 로고
    • Cross platform microarray analysis for robust identification of differentially expressed genes
    • Bosotti,R. et al. (2007) Cross platform microarray analysis for robust identification of differentially expressed genes. BMC Bioinformatics, 8 (Suppl. 1), S5.
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 1
    • Bosotti, R.1
  • 6
    • 0037499970 scopus 로고    scopus 로고
    • MatchMiner: a tool for batch navigation among gene and gene product identifiers
    • Bussey,K.J. et al. (2003) MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol., 4, R27.
    • (2003) Genome Biol. , vol.4
    • Bussey, K.J.1
  • 7
    • 33845345622 scopus 로고    scopus 로고
    • A rapid method for microarray cross platform comparisons using gene expression signatures
    • Cheadle,C. et al. (2007) A rapid method for microarray cross platform comparisons using gene expression signatures. Mol. Cell Probes, 21, 35-46.
    • (2007) Mol. Cell Probes , vol.21 , pp. 35-46
    • Cheadle, C.1
  • 8
    • 67649197934 scopus 로고    scopus 로고
    • Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction
    • Cheng,C. et al. (2009) Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction. Bioinformatics, 25, 1655-1661.
    • (2009) Bioinformatics , vol.25 , pp. 1655-1661
    • Cheng, C.1
  • 11
    • 0035939903 scopus 로고    scopus 로고
    • Delineation of prognostic biomarkers in prostate cancer
    • Dhanasekaran,S.M. et al. (2001) Delineation of prognostic biomarkers in prostate cancer. Nature, 412, 822-826.
    • (2001) Nature , vol.412 , pp. 822-826
    • Dhanasekaran, S.M.1
  • 12
    • 19544383638 scopus 로고    scopus 로고
    • Sample size determination in microarray experiments for class comparison and prognostic classification
    • Dobbin,K. and Simon,R. (2005) Sample size determination in microarray experiments for class comparison and prognostic classification. Biostatistics, 6, 27-38.
    • (2005) Biostatistics , vol.6 , pp. 27-38
    • Dobbin, K.1    Simon, R.2
  • 13
    • 40749107034 scopus 로고    scopus 로고
    • How large a training set is needed to develop a classifier for microarray data?
    • Dobbin,K.K. et al. (2008) How large a training set is needed to develop a classifier for microarray data? Clin. Cancer Res., 14, 108-114.
    • (2008) Clin. Cancer Res , vol.14 , pp. 108-114
    • Dobbin, K.K.1
  • 14
    • 13444282534 scopus 로고    scopus 로고
    • Outcome signature genes in breast cancer: is there a unique set?
    • Ein-Dor,L. et al. (2005) Outcome signature genes in breast cancer: is there a unique set? Bioinformatics, 21, 171-178.
    • (2005) Bioinformatics , vol.21 , pp. 171-178
    • Ein-Dor, L.1
  • 15
    • 0035923583 scopus 로고    scopus 로고
    • Diversity of gene expression in adenocarcinoma of the lung
    • Garber,M.E. et al. (2001) Diversity of gene expression in adenocarcinoma of the lung. Proc. Natl Acad. Sci. USA, 98, 13784-13789.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 13784-13789
    • Garber, M.E.1
  • 16
    • 0036161259 scopus 로고    scopus 로고
    • Gene selection for cancer classification using support vector machines
    • Guyon,I. et al. (2002) Gene selection for cancer classification using support vector machines. Mach. Learn., 46, 389-422.
    • (2002) Mach. Learn. , vol.46 , pp. 389-422
    • Guyon, I.1
  • 17
    • 0001138328 scopus 로고
    • A K-means clustering algorithm
    • Hartigan,J.A. and Wong,M.A. (1979) A K-means clustering algorithm. Appl. Stat.,28, 100-108.
    • (1979) Appl. Stat. , vol.28 , pp. 100-108
    • Hartigan, J.A.1    Wong, M.A.2
  • 18
    • 0038244058 scopus 로고    scopus 로고
    • Gene expression predictors of breast cancer outcomes
    • Huang,E. et al. (2003) Gene expression predictors of breast cancer outcomes. Lancet, 361, 1590-1596.
    • (2003) Lancet , vol.361 , pp. 1590-1596
    • Huang, E.1
  • 19
    • 18244384210 scopus 로고    scopus 로고
    • Multiple-laboratory comparison of microarray platforms
    • Irizarry,R.A. et al. (2005) Multiple-laboratory comparison of microarray platforms. Nat. Methods, 2, 345-350.
    • (2005) Nat. Methods , vol.2 , pp. 345-350
    • Irizarry, R.A.1
  • 20
    • 41149167129 scopus 로고    scopus 로고
    • Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package annotationTools
    • Kuhn,A. et al. (2008) Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package annotationTools. BMC Bioinformatics, 9, 26.
    • (2008) BMC Bioinformatics , vol.9 , pp. 26
    • Kuhn, A.1
  • 21
    • 33748961513 scopus 로고    scopus 로고
    • A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets
    • Lai,C. et al. (2006) A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets. BMC Bioinformatics, 7, 235.
    • (2006) BMC Bioinformatics , vol.7 , pp. 235
    • Lai, C.1
  • 22
    • 0035874995 scopus 로고    scopus 로고
    • Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling
    • Luo,J. et al. (2001) Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling. Cancer Res., 61, 4683-4688.
    • (2001) Cancer Res. , vol.61 , pp. 4683-4688
    • Luo, J.1
  • 24
    • 33745736739 scopus 로고    scopus 로고
    • Cross-platform classification in microarray-based leukemia diagnostics
    • Nilsson,B. et al. (2006) Cross-platform classification in microarray-based leukemia diagnostics. Haematologica, 91, 821-824.
    • (2006) Haematologica , vol.91 , pp. 821-824
    • Nilsson, B.1
  • 25
    • 34147177060 scopus 로고    scopus 로고
    • Averaged gene expressions for regression
    • Park,M.Y. et al. (2007) Averaged gene expressions for regression. Biostatistics, 8, 212-227.
    • (2007) Biostatistics , vol.8 , pp. 212-227
    • Park, M.Y.1
  • 26
    • 4143151607 scopus 로고    scopus 로고
    • Current issues for DNAmicroarrays: platform comparison, double linear amplification, and universal RNA reference
    • Park,P.J. et al. (2004) Current issues for DNAmicroarrays: platform comparison, double linear amplification, and universal RNA reference. J. Biotechnol., 112, 225-245.
    • (2004) J. Biotechnol. , vol.112 , pp. 225-245
    • Park, P.J.1
  • 27
    • 2942534096 scopus 로고    scopus 로고
    • Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes
    • Pittman,J. et al. (2004) Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes. Proc. Natl Acad. Sci. USA, 101, 8431-8436.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 8431-8436
    • Pittman, J.1
  • 28
    • 33746875641 scopus 로고    scopus 로고
    • Agenomic strategy to refine prognosis in early-stage non-small-cell lung cancer
    • Potti,A. etal. (2006)Agenomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N. Engl. J. Med., 355, 570-580.
    • (2006) N. Engl. J. Med. , vol.355 , pp. 570-580
    • Potti, A.1
  • 29
    • 48349087525 scopus 로고    scopus 로고
    • Promises and caveats of in silico biomarker discovery
    • Pusztai,L. and Leyland-Jones,B. (2008) Promises and caveats of in silico biomarker discovery. Br. J. Cancer, 99, 385-386.
    • (2008) Br. J. Cancer , vol.99 , pp. 385-386
    • Pusztai, L.1    Leyland-Jones, B.2
  • 30
    • 0037226593 scopus 로고    scopus 로고
    • Amolecular signature of metastasis in primary solid tumors
    • Ramaswamy,S. et al. (2003) Amolecular signature of metastasis in primary solid tumors. Nat. Genet., 33, 49-54.
    • (2003) Nat. Genet. , vol.33 , pp. 49-54
    • Ramaswamy, S.1
  • 31
    • 6944244084 scopus 로고    scopus 로고
    • Amodule map showing conditional activity of expression modules in cancer
    • Segal,E. et al. (2004)Amodule map showing conditional activity of expression modules in cancer. Nat. Genet., 36, 1090-1098.
    • (2004) Nat. Genet. , vol.36 , pp. 1090-1098
    • Segal, E.1
  • 32
    • 27644528185 scopus 로고    scopus 로고
    • Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential
    • Shi,L. et al. (2005) Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics, 6 (Suppl. 2), S12.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 2
    • Shi, L.1
  • 33
    • 8444246272 scopus 로고    scopus 로고
    • QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies
    • Shi,L. et al. (2004) QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev. Mol. Diagn., 4, 761-777.
    • (2004) Expert Rev. Mol. Diagn. , vol.4 , pp. 761-777
    • Shi, L.1
  • 34
    • 0035845511 scopus 로고    scopus 로고
    • Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
    • Sorlie,T. et al. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA, 98, 10869-10874.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 10869-10874
    • Sorlie, T.1
  • 35
    • 0036457915 scopus 로고    scopus 로고
    • Prediction and uncertainty in the analysis of gene expression profiles
    • Spang,R. et al. (2002) Prediction and uncertainty in the analysis of gene expression profiles. In Silico Biol., 2, 369-381.
    • (2002) In Silico Biol. , vol.2 , pp. 369-381
    • Spang, R.1
  • 36
    • 34347219009 scopus 로고    scopus 로고
    • Metagene projection for cross-platform, cross-species characterization of global transcriptional states
    • Tamayo,P. et al. (2007) Metagene projection for cross-platform, cross-species characterization of global transcriptional states. Proc. Natl Acad. Sci. USA, 104, 5959-5964.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 5959-5964
    • Tamayo, P.1
  • 37
    • 0141905890 scopus 로고    scopus 로고
    • Evaluation of gene expression measurements from commercial microarray platforms
    • Tan,P.K. et al. (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res., 31, 5676-5684.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5676-5684
    • Tan, P.K.1
  • 38
    • 33750021210 scopus 로고    scopus 로고
    • Evaluation and comparison of gene clustering methods in microarray analysis
    • Thalamuthu,A. et al. (2006) Evaluation and comparison of gene clustering methods in microarray analysis. Bioinformatics, 22, 2405-2412.
    • (2006) Bioinformatics , vol.22 , pp. 2405-2412
    • Thalamuthu, A.1
  • 39
    • 0037076272 scopus 로고    scopus 로고
    • Diagnosis of multiple cancer types by shrunken centroids of gene expression
    • Tibshirani,R. et al. (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl Acad. Sci. USA, 99, 6567-6572.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 6567-6572
    • Tibshirani, R.1
  • 40
    • 34548784943 scopus 로고    scopus 로고
    • Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data
    • Tseng,G.C. (2007) Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data. Bioinformatics, 23, 2247-2255.
    • (2007) Bioinformatics , vol.23 , pp. 2247-2255
    • Tseng, G.C.1
  • 41
    • 15044346962 scopus 로고    scopus 로고
    • Tight clustering: a resampling-based approach for identifying stable and tight patterns in data
    • Tseng,G.C. and Wong,W.H. (2005) Tight clustering: a resampling-based approach for identifying stable and tight patterns in data. Biometrics, 61, 10-16.
    • (2005) Biometrics , vol.61 , pp. 10-16
    • Tseng, G.C.1    Wong, W.H.2
  • 42
    • 18244409687 scopus 로고    scopus 로고
    • Gene expression profiling predicts clinical outcome of breast cancer
    • van't Veer,L.J. et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530-536.
    • (2002) Nature , vol.415 , pp. 530-536
    • van't Veer, L.J.1
  • 43
    • 42349111720 scopus 로고    scopus 로고
    • Module-based outcome prediction using breast cancer compendia
    • van Vliet,M.H. et al. (2007) Module-based outcome prediction using breast cancer compendia. PLoS ONE, 2, e1047.
    • (2007) PLoS ONE , vol.2
    • van Vliet, M.H.1
  • 44
    • 0035881732 scopus 로고    scopus 로고
    • Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer
    • Welsh,J.B. et al. (2001) Analysis of gene expression identifies candidate markers and pharmacological targets in prostate cancer. Cancer Res., 61, 5974-5978.
    • (2001) Cancer Res. , vol.61 , pp. 5974-5978
    • Welsh, J.B.1
  • 45
    • 0035949684 scopus 로고    scopus 로고
    • Predicting the clinical status of human breast cancer by using gene expression profiles
    • West,M. et al. (2001) Predicting the clinical status of human breast cancer by using gene expression profiles. Proc. Natl Acad. Sci. USA, 98, 11462-11467.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 11462-11467
    • West, M.1
  • 46
    • 33745145845 scopus 로고    scopus 로고
    • Embracing the complexity of genomic data for personalized medicine
    • West,M. et al. (2006) Embracing the complexity of genomic data for personalized medicine. Genome Res., 16, 559-566.
    • (2006) Genome Res. , vol.16 , pp. 559-566
    • West, M.1
  • 47
    • 39049127598 scopus 로고    scopus 로고
    • Revealing targeted therapy for human cancer by gene module maps
    • Wong,D.J. et al. (2008) Revealing targeted therapy for human cancer by gene module maps. Cancer Res., 68, 369-378.
    • (2008) Cancer Res. , vol.68 , pp. 369-378
    • Wong, D.J.1
  • 48
    • 4344561557 scopus 로고    scopus 로고
    • Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy
    • Yu,Y.P. et al. (2004) Gene expression alterations in prostate cancer predicting tumor aggression and preceding development of malignancy. J. Clin. Oncol., 22, 2790-2799.
    • (2004) J. Clin. Oncol. , vol.22 , pp. 2790-2799
    • Yu, Y.P.1
  • 49
    • 33646377650 scopus 로고    scopus 로고
    • Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data
    • Zhang,X. et al. (2006) Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data. BMC Bioinformatics, 7, 197.
    • (2006) BMC Bioinformatics , vol.7 , pp. 197
    • Zhang, X.1


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