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Volumn 28, Issue , 2012, Pages 39-66

Statistical Analysis of Gene Expression Studies with Ordered Experimental Conditions

Author keywords

Cell cycle; Dose response; Gene expression; Microarray; Multiple comparisons; Order restricted inference; Time course

Indexed keywords


EID: 84866300749     PISSN: 01697161     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-44-451875-0.00003-8     Document Type: Chapter
Times cited : (4)

References (87)
  • 1
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Alter O., Brown P., Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. 2000, 97:10101-10106.
    • (2000) Proc. Natl. Acad. Sci. , vol.97 , pp. 10101-10106
    • Alter, O.1    Brown, P.2    Botstein, D.3
  • 3
    • 55449128330 scopus 로고    scopus 로고
    • BATS: a Bayesian user-friendly software for analyzing time series microarray experiments
    • Angelini C., Cutillo L., De Candidiis D., Mutarelli M., Pensky M. BATS: a Bayesian user-friendly software for analyzing time series microarray experiments. BMC Bioinform. 2008, 9:415.
    • (2008) BMC Bioinform. , vol.9 , pp. 415
    • Angelini, C.1    Cutillo, L.2    De Candidiis, D.3    Mutarelli, M.4    Pensky, M.5
  • 4
    • 16344369007 scopus 로고    scopus 로고
    • Clustering of gene experssion data using a local shape-based similarity measure
    • Balasubramaniyan R., Hullermeier E., Weskamp N., Kamper J. Clustering of gene experssion data using a local shape-based similarity measure. Bioinformatics 2005, 21:1069-1077.
    • (2005) Bioinformatics , vol.21 , pp. 1069-1077
    • Balasubramaniyan, R.1    Hullermeier, E.2    Weskamp, N.3    Kamper, J.4
  • 6
    • 0042838381 scopus 로고    scopus 로고
    • Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes
    • Bar-Joseph Z., Gerber G., Simon I., Gifford D.K., Jaakkola T.S. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proc. Natl. Acad. Sci. 2003, 100:10146-10151.
    • (2003) Proc. Natl. Acad. Sci. , vol.100 , pp. 10146-10151
    • Bar-Joseph, Z.1    Gerber, G.2    Simon, I.3    Gifford, D.K.4    Jaakkola, T.S.5
  • 7
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. Ser. B 1995, 57:289-300.
    • (1995) J. Roy. Stat. Soc. Ser. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 8
    • 0035733108 scopus 로고    scopus 로고
    • The control of the false discovery rate in multiple testing under dependency
    • Benjamini Y., Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 2001, 29:1165-1188.
    • (2001) Ann. Stat. , vol.29 , pp. 1165-1188
    • Benjamini, Y.1    Yekutieli, D.2
  • 10
    • 26944440912 scopus 로고    scopus 로고
    • Hepatic gene expression changes throughout the day in the Fischer rat: implications for toxicogenomic experiments
    • Boorman G., Blackshear P., Parker J., Lobenhofer E., Malarky D., Vallant M., Gerken D., Irwin R. Hepatic gene expression changes throughout the day in the Fischer rat: implications for toxicogenomic experiments. Toxicol. Sci. 2005, 86(1):85-193.
    • (2005) Toxicol. Sci. , vol.86 , Issue.1 , pp. 85-193
    • Boorman, G.1    Blackshear, P.2    Parker, J.3    Lobenhofer, E.4    Malarky, D.5    Vallant, M.6    Gerken, D.7    Irwin, R.8
  • 12
    • 4243071596 scopus 로고    scopus 로고
    • The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    • Bozdech Z., Llinás M., Pulliam B.L., Wong E.D., Zhu J., DeRisi J.L. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLOS Biol. 2003, 1:1-16.
    • (2003) PLOS Biol. , vol.1 , pp. 1-16
    • Bozdech, Z.1    Llinás, M.2    Pulliam, B.L.3    Wong, E.D.4    Zhu, J.5    DeRisi, J.L.6
  • 14
    • 0032356568 scopus 로고    scopus 로고
    • Smoothing spline models for the analysis of nested and crossed samples of curves
    • Brumback B.A., Rice J.A. Smoothing spline models for the analysis of nested and crossed samples of curves. J. Am. Stat. Assoc. 1998, 93:961-976.
    • (1998) J. Am. Stat. Assoc. , vol.93 , pp. 961-976
    • Brumback, B.A.1    Rice, J.A.2
  • 15
    • 0031246430 scopus 로고    scopus 로고
    • Ratio-based decisions and the quantitative analysis of cDNA microarray images
    • Chen Y., Dougherty E., Bittner M. Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Opt. 1997, 2:364-374.
    • (1997) J. Biomed. Opt. , vol.2 , pp. 364-374
    • Chen, Y.1    Dougherty, E.2    Bittner, M.3
  • 16
    • 4444339832 scopus 로고    scopus 로고
    • Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle
    • Chen H.-C., Lee H.-C, Lin T.-Y., Li W.-H., Chen B.-S. Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle. Bioinformatics 2004, 20:1914-1927.
    • (2004) Bioinformatics , vol.20 , pp. 1914-1927
    • Chen, H.-C.1    Lee, H.-C.2    Lin, T.-Y.3    Li, W.-H.4    Chen, B.-S.5
  • 17
    • 38049181106 scopus 로고    scopus 로고
    • Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes
    • Chou J., Zhou T., Kaufmann W., Paules R., Bushel P. Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes. BMC Bioinform. 2007, 8:427.
    • (2007) BMC Bioinform. , vol.8 , pp. 427
    • Chou, J.1    Zhou, T.2    Kaufmann, W.3    Paules, R.4    Bushel, P.5
  • 19
    • 35148853808 scopus 로고    scopus 로고
    • SAM Significance Analysis of Microarrays Users Guide and Technical Document
    • Chu, G., Narasimhan, B., Tibshirani, R., Tusher, V., 2002. SAM Significance Analysis of Microarrays Users Guide and Technical Document. http://www-stat.stanford.edu/~tibs/SAM/.
    • (2002)
    • Chu, G.1    Narasimhan, B.2    Tibshirani, R.3    Tusher, V.4
  • 20
    • 3943113640 scopus 로고    scopus 로고
    • Using ANOVA to analyze microarray data
    • Churchill G.A. Using ANOVA to analyze microarray data. BioTechniques 2004, 37:173-177.
    • (2004) BioTechniques , vol.37 , pp. 173-177
    • Churchill, G.A.1
  • 21
    • 33646147811 scopus 로고    scopus 로고
    • MaSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
    • Conesa A., Nueda M.J., Ferrer A., Talón M. maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics 2006, 22:1096-1102.
    • (2006) Bioinformatics , vol.22 , pp. 1096-1102
    • Conesa, A.1    Nueda, M.J.2    Ferrer, A.3    Talón, M.4
  • 23
    • 0036855903 scopus 로고    scopus 로고
    • Statistical analysis of a small set of time-ordered gene expression data using linear splines
    • de Hoon M., Imoto S., Miyano S. Statistical analysis of a small set of time-ordered gene expression data using linear splines. Bioinformatics 2002, 18:1477-1485.
    • (2002) Bioinformatics , vol.18 , pp. 1477-1485
    • de Hoon, M.1    Imoto, S.2    Miyano, S.3
  • 24
    • 0013080197 scopus 로고    scopus 로고
    • Circular regression
    • Downs T.D., Mardia K.V. Circular regression. Biometrika 2002, 89:683-697.
    • (2002) Biometrika , vol.89 , pp. 683-697
    • Downs, T.D.1    Mardia, K.V.2
  • 25
    • 0036489046 scopus 로고    scopus 로고
    • Comparison of discrimination methods for the classification of tumors using gene expression data
    • Dudoit S., Fridyland J., Speed T.P. Comparison of discrimination methods for the classification of tumors using gene expression data. J. Am. Stat. Assoc. 2002, 97:77-87.
    • (2002) J. Am. Stat. Assoc. , vol.97 , pp. 77-87
    • Dudoit, S.1    Fridyland, J.2    Speed, T.P.3
  • 26
    • 0032441150 scopus 로고    scopus 로고
    • Cluster analysis and display of genome-wide expression patterns
    • Eisen M., Spellman P., Brown P., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. 1998, 95:14863-14868.
    • (1998) Proc. Natl. Acad. Sci. , vol.95 , pp. 14863-14868
    • Eisen, M.1    Spellman, P.2    Brown, P.3    Botstein, D.4
  • 27
    • 28644452470 scopus 로고    scopus 로고
    • Clustering short time series gene expression data
    • Ernst J., Nau G., Bar-Joseph Z. Clustering short time series gene expression data. Bioinformatics 2005, 21:159-168.
    • (2005) Bioinformatics , vol.21 , pp. 159-168
    • Ernst, J.1    Nau, G.2    Bar-Joseph, Z.3
  • 28
    • 13944282531 scopus 로고    scopus 로고
    • A time course microarray study of gene expression in the mouse lacrimal gland after acute corneal trauma
    • Fang Y., Choi D., Searles R.P., Mathers W.D. A time course microarray study of gene expression in the mouse lacrimal gland after acute corneal trauma. Invest. Opthalmol. Vis. Sci. 2005, 46(2):461-469.
    • (2005) Invest. Opthalmol. Vis. Sci. , vol.46 , Issue.2 , pp. 461-469
    • Fang, Y.1    Choi, D.2    Searles, R.P.3    Mathers, W.D.4
  • 29
    • 33745646143 scopus 로고    scopus 로고
    • Incorporating additional information to normal linear discriminant rules
    • Fernandez M., Rueda C., Salvador B. Incorporating additional information to normal linear discriminant rules. J. Am. Stat. Assoc. 2006, 101:569-577.
    • (2006) J. Am. Stat. Assoc. , vol.101 , pp. 569-577
    • Fernandez, M.1    Rueda, C.2    Salvador, B.3
  • 30
    • 84860200052 scopus 로고    scopus 로고
    • Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species
    • Fernandez M., Rueda C., Peddada S. Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species. Nucleic Acids Res. 2012, 40(7):2823-2832.
    • (2012) Nucleic Acids Res. , vol.40 , Issue.7 , pp. 2823-2832
    • Fernandez, M.1    Rueda, C.2    Peddada, S.3
  • 33
    • 48849111904 scopus 로고    scopus 로고
    • Adaptive choice of the number of bootstrap samples in large scale multiple testing
    • Art. 13
    • Guo W., Peddada S. Adaptive choice of the number of bootstrap samples in large scale multiple testing. Stat. Appl. Genet. Mol. Biol. 2008, 7(1). Art. 13.
    • (2008) Stat. Appl. Genet. Mol. Biol. , vol.7 , Issue.1
    • Guo, W.1    Peddada, S.2
  • 34
    • 77953019375 scopus 로고    scopus 로고
    • Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories
    • Guo W., Sarkar S.K., Peddada S.D. Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories. Biometrics 2010, 66:485-492.
    • (2010) Biometrics , vol.66 , pp. 485-492
    • Guo, W.1    Sarkar, S.K.2    Peddada, S.D.3
  • 35
    • 0141850391 scopus 로고    scopus 로고
    • Significance analysis of longitudinal gene expression data
    • Guo X., Qi H., Verfaillie C.M., Pan W. Significance analysis of longitudinal gene expression data. Bioinformatics 2003, 19:1628-1635.
    • (2003) Bioinformatics , vol.19 , pp. 1628-1635
    • Guo, X.1    Qi, H.2    Verfaillie, C.M.3    Pan, W.4
  • 36
    • 0032729435 scopus 로고    scopus 로고
    • Exploring expression data: identification and analysis of co-expressed genes
    • Heyer L., Kruglyak S., Yooseph S. Exploring expression data: identification and analysis of co-expressed genes. Genome Res. 1999, 9:1106-1115.
    • (1999) Genome Res. , vol.9 , pp. 1106-1115
    • Heyer, L.1    Kruglyak, S.2    Yooseph, S.3
  • 38
    • 33745242945 scopus 로고    scopus 로고
    • Functional hierarchical models for identifying genes with different time-course expression profiles
    • Hong F., Li H. Functional hierarchical models for identifying genes with different time-course expression profiles. Biometrics 2006, 62:534-544.
    • (2006) Biometrics , vol.62 , pp. 534-544
    • Hong, F.1    Li, H.2
  • 39
    • 21344486796 scopus 로고
    • Confidence interval estimation subject to order restrictions
    • Hwang J.T.G., Peddada S.D. Confidence interval estimation subject to order restrictions. Ann. Stat. 1994, 22:67-93.
    • (1994) Ann. Stat. , vol.22 , pp. 67-93
    • Hwang, J.T.G.1    Peddada, S.D.2
  • 40
    • 0042744696 scopus 로고    scopus 로고
    • Detecting differentially expressed genes in microarrays using Bayesian model selection
    • Ishwaran H., Rao J. Detecting differentially expressed genes in microarrays using Bayesian model selection. J. Am. Stat. Assoc. 2003, 98:438-455.
    • (2003) J. Am. Stat. Assoc. , vol.98 , pp. 438-455
    • Ishwaran, H.1    Rao, J.2
  • 41
    • 22944460748 scopus 로고    scopus 로고
    • Spike and slab variable selection: frequentist and Bayesian strategies
    • Ishwaran H., Rao J. Spike and slab variable selection: frequentist and Bayesian strategies. Ann. Stat. 2005, 33:730-773.
    • (2005) Ann. Stat. , vol.33 , pp. 730-773
    • Ishwaran, H.1    Rao, J.2
  • 42
    • 33644583716 scopus 로고    scopus 로고
    • BAMarray™: Java software for Bayesian analysis of variance for microarray data
    • Ishwaran H., Rao J.S., Kogalur U.B. BAMarray™: Java software for Bayesian analysis of variance for microarray data. BMC Bioinform. 2006, 7:59.
    • (2006) BMC Bioinform. , vol.7 , pp. 59
    • Ishwaran, H.1    Rao, J.S.2    Kogalur, U.B.3
  • 44
    • 33845756231 scopus 로고    scopus 로고
    • A two-step multiple comparison procedure for a large number of tests and multiple treatments
    • Epub December 18, 2006
    • Jiang H., Doerge R.W. A two-step multiple comparison procedure for a large number of tests and multiple treatments. Stat. Appl. Genet. Mol. Biol. 2004, 5:28. Epub December 18, 2006.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.5 , pp. 28
    • Jiang, H.1    Doerge, R.W.2
  • 45
    • 0035733752 scopus 로고    scopus 로고
    • The contributions of sex, genotype, and age to transcriptional variance in Drosophila melanogaster
    • Jin W., Riley R.M., Wolfinger R.D., White K.P., Passador-Gurgel G., Gibson G. The contributions of sex, genotype, and age to transcriptional variance in Drosophila melanogaster. Nature Genet. 2001, 29:389-395.
    • (2001) Nature Genet. , vol.29 , pp. 389-395
    • Jin, W.1    Riley, R.M.2    Wolfinger, R.D.3    White, K.P.4    Passador-Gurgel, G.5    Gibson, G.6
  • 46
    • 0037343132 scopus 로고    scopus 로고
    • A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription
    • Johansson D., Lindgren P., Berglund A. A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcription. Bioinformatics 2003, 19:467-473.
    • (2003) Bioinformatics , vol.19 , pp. 467-473
    • Johansson, D.1    Lindgren, P.2    Berglund, A.3
  • 47
    • 0035032570 scopus 로고    scopus 로고
    • Statistical design and the analysis of gene expression microarray data
    • Kerr K., Churchill G. Statistical design and the analysis of gene expression microarray data. Genet. Res. Camb. 2001, 77:123-128.
    • (2001) Genet. Res. Camb. , vol.77 , pp. 123-128
    • Kerr, K.1    Churchill, G.2
  • 48
    • 0035979259 scopus 로고    scopus 로고
    • Bootstrapping cluster analysis: assessing reliability of conclusions from microarray experiments
    • Kerr K., Churchill G. Bootstrapping cluster analysis: assessing reliability of conclusions from microarray experiments. Proc. Natl. Acad. Sci. 2001, 98:8961-8965.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 8961-8965
    • Kerr, K.1    Churchill, G.2
  • 49
    • 58149330805 scopus 로고    scopus 로고
    • A computational approach to the functional clustering of periodic gene-expression profiles
    • Kim B.-R., Zhang L., Berg A., Fan J., Wu R. A computational approach to the functional clustering of periodic gene-expression profiles. Genetics 2008, 180:821-834.
    • (2008) Genetics , vol.180 , pp. 821-834
    • Kim, B.-R.1    Zhang, L.2    Berg, A.3    Fan, J.4    Wu, R.5
  • 50
    • 0000181737 scopus 로고
    • The jackknife and the bootstrap for general stationary observations
    • Kunsch H.R. The jackknife and the bootstrap for general stationary observations. Ann. Stat. 1989, 17:1217-1241.
    • (1989) Ann. Stat. , vol.17 , pp. 1217-1241
    • Kunsch, H.R.1
  • 51
    • 32544433476 scopus 로고    scopus 로고
    • EDGE: extraction and analysis of differential gene expression
    • Leek J.T., Monsen E., Dabney A.R., Storey J.D. EDGE: extraction and analysis of differential gene expression. Bioinformatics 2006, 22:507-508.
    • (2006) Bioinformatics , vol.22 , pp. 507-508
    • Leek, J.T.1    Monsen, E.2    Dabney, A.R.3    Storey, J.D.4
  • 52
    • 0036139278 scopus 로고    scopus 로고
    • Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method
    • Li.L., Weinberg C., Darden T., Pederson L. Gene selection for sample classification based on gene expression data: study of sensitivity to choice of parameters of the GA/KNN method. Bioinformatics 2001, 17:1131-1142.
    • (2001) Bioinformatics , vol.17 , pp. 1131-1142
    • Li, L.1    Weinberg, C.2    Darden, T.3    Pederson, L.4
  • 53
    • 0036583328 scopus 로고    scopus 로고
    • Statistical methods for analysis of time-course gene expression data
    • Li H., Luan Y., Hong F., Li Y. Statistical methods for analysis of time-course gene expression data. Front. Biosci. 2002, 7:a90-a98.
    • (2002) Front. Biosci. , vol.7
    • Li, H.1    Luan, Y.2    Hong, F.3    Li, Y.4
  • 54
    • 21444457867 scopus 로고    scopus 로고
    • Differential and trajectory methods for time course gene expression data
    • Liang Y., Tayo B., Cai X., Keleman A. Differential and trajectory methods for time course gene expression data. Bioinformatics 2005, 21:3009-3016.
    • (2005) Bioinformatics , vol.21 , pp. 3009-3016
    • Liang, Y.1    Tayo, B.2    Cai, X.3    Keleman, A.4
  • 56
    • 8844266856 scopus 로고    scopus 로고
    • A geometric approach to determine association and coherence of the activation times of cell-cycling genes under different experimental conditions
    • Liu D., Weinberg C., Peddada S.D. A geometric approach to determine association and coherence of the activation times of cell-cycling genes under different experimental conditions. Bioinformatics 2004, 20:2521-2528.
    • (2004) Bioinformatics , vol.20 , pp. 2521-2528
    • Liu, D.1    Weinberg, C.2    Peddada, S.D.3
  • 57
    • 25444533041 scopus 로고    scopus 로고
    • Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray
    • Liu H., Tarima S., Borders A., Getchell T., Getchell M., Stromberg A. Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray. BMC Bioinform. 2005, 6:106.
    • (2005) BMC Bioinform. , vol.6 , pp. 106
    • Liu, H.1    Tarima, S.2    Borders, A.3    Getchell, T.4    Getchell, M.5    Stromberg, A.6
  • 59
    • 13644271264 scopus 로고    scopus 로고
    • A two-step strategy for detecting differential gene expression in cDNA microarray data
    • Lu Y., Zhu J., Liu P. A two-step strategy for detecting differential gene expression in cDNA microarray data. Current Genet. 2005, 47(2):121-131.
    • (2005) Current Genet. , vol.47 , Issue.2 , pp. 121-131
    • Lu, Y.1    Zhu, J.2    Liu, P.3
  • 60
    • 0037339264 scopus 로고    scopus 로고
    • Clustering of time-course gene expression data using a mixed-effects model with B-splines
    • Luan Y., Li H. Clustering of time-course gene expression data using a mixed-effects model with B-splines. Bioinformatics 2003, 19:474-482.
    • (2003) Bioinformatics , vol.19 , pp. 474-482
    • Luan, Y.1    Li, H.2
  • 61
    • 1342288029 scopus 로고    scopus 로고
    • Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data
    • Luan Y., Li H. Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data. Bioinformatics 2004, 20:332-339.
    • (2004) Bioinformatics , vol.20 , pp. 332-339
    • Luan, Y.1    Li, H.2
  • 64
    • 22744437234 scopus 로고    scopus 로고
    • The cell cycle-regulated genes of Schizosaccharomyces pombe
    • Oliva A., et al. The cell cycle-regulated genes of Schizosaccharomyces pombe. PLOS Biol. 2005, 3:1239-1260.
    • (2005) PLOS Biol. , vol.3 , pp. 1239-1260
    • Oliva, A.1
  • 65
    • 0037433769 scopus 로고    scopus 로고
    • Statistical tests for identifying differentially expressed genes in time-course microarray experiments
    • Park T., Yi S.-G., Lee S., Lee S.Y., Yoo D.-H., Ahn J.-I., Lee Y.-S. Statistical tests for identifying differentially expressed genes in time-course microarray experiments. Bioinformatics 2003, 19:694-703.
    • (2003) Bioinformatics , vol.19 , pp. 694-703
    • Park, T.1    Yi, S.-G.2    Lee, S.3    Lee, S.Y.4    Yoo, D.-H.5    Ahn, J.-I.6    Lee, Y.-S.7
  • 66
    • 0037620663 scopus 로고    scopus 로고
    • Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference
    • Peddada S.D., Lobenhofer E., Li L., Afshari C., Weinberg C.R., Umbach D.M. Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference. Bioinformatics 2003, 19:834-841.
    • (2003) Bioinformatics , vol.19 , pp. 834-841
    • Peddada, S.D.1    Lobenhofer, E.2    Li, L.3    Afshari, C.4    Weinberg, C.R.5    Umbach, D.M.6
  • 67
    • 27544514952 scopus 로고    scopus 로고
    • ORIOGEN: order restricted inference for ordered gene expression
    • Peddada S.D., Harris S., Zajd J., Harvey E. ORIOGEN: order restricted inference for ordered gene expression. Bioinformatics 2005, 21:3933-3934.
    • (2005) Bioinformatics , vol.21 , pp. 3933-3934
    • Peddada, S.D.1    Harris, S.2    Zajd, J.3    Harvey, E.4
  • 68
    • 78650106545 scopus 로고    scopus 로고
    • Analysis of correlated gene expression data on ordered categories
    • Peddada S.D., Harris S., Davidov O. Analysis of correlated gene expression data on ordered categories. J. Ind. Soc. Agric. Stat. 2010, 64:45-60.
    • (2010) J. Ind. Soc. Agric. Stat. , vol.64 , pp. 45-60
    • Peddada, S.D.1    Harris, S.2    Davidov, O.3
  • 69
    • 20044366888 scopus 로고    scopus 로고
    • Identification of cell cycle-regulated genes in fission yeast
    • Peng X., et al. Identification of cell cycle-regulated genes in fission yeast. Mol. Biol. Cell 2005, 16:1026-1042.
    • (2005) Mol. Biol. Cell , vol.16 , pp. 1026-1042
    • Peng, X.1
  • 71
    • 70350341224 scopus 로고    scopus 로고
    • Estimation of parameters subject to order restrictions on a circle with application to estimation of phase angles of cell cycle genes
    • Rueda C., Fernandez M.A., Peddada S.D. Estimation of parameters subject to order restrictions on a circle with application to estimation of phase angles of cell cycle genes. J. Am. Stat. Assoc. 2009, 104:338-347.
    • (2009) J. Am. Stat. Assoc. , vol.104 , pp. 338-347
    • Rueda, C.1    Fernandez, M.A.2    Peddada, S.D.3
  • 72
    • 3543042493 scopus 로고    scopus 로고
    • Periodic gene expression program of the fission yeast cell cycle
    • Rustici G., et al. Periodic gene expression program of the fission yeast cell cycle. Nature Genet. 2004, 36:809-817.
    • (2004) Nature Genet. , vol.36 , pp. 809-817
    • Rustici, G.1
  • 74
    • 0036173128 scopus 로고    scopus 로고
    • Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development
    • ŜáŜik R., Iranfar N., Hwa T., Loomis W.F. Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development. Bioinformatics 2002, 18:61-66.
    • (2002) Bioinformatics , vol.18 , pp. 61-66
    • ŜáŜik, R.1    Iranfar, N.2    Hwa, T.3    Loomis, W.F.4
  • 75
    • 26244460973 scopus 로고    scopus 로고
    • Analysis of calcium-inducible genes in keratinocytes using suppression subtractive hybridization and cDNA microarray
    • Seo E., Namkung J., Lee W., Im M., Kee S., Tae P., Yang J., Seo Y., Park J., Deok K., Lee J. Analysis of calcium-inducible genes in keratinocytes using suppression subtractive hybridization and cDNA microarray. Genomics 2005, 86:528-538.
    • (2005) Genomics , vol.86 , pp. 528-538
    • Seo, E.1    Namkung, J.2    Lee, W.3    Im, M.4    Kee, S.5    Tae, P.6    Yang, J.7    Seo, Y.8    Park, J.9    Deok, K.10    Lee, J.11
  • 76
    • 84866299020 scopus 로고    scopus 로고
    • Order-restricted inference for ordered gene expression (ORIOGEN) data under heteroscedastic variances
    • Simmons S., Peddada S.D. Order-restricted inference for ordered gene expression (ORIOGEN) data under heteroscedastic variances. Bioinformation 2007, 1(10):414-419.
    • (2007) Bioinformation , vol.1 , Issue.10 , pp. 414-419
    • Simmons, S.1    Peddada, S.D.2
  • 77
    • 34447649358 scopus 로고    scopus 로고
    • Clustering of time-course gene expression data using functional data analysis
    • Song J.J., Lee H.-J., Morris J.S., Kang S. Clustering of time-course gene expression data using functional data analysis. Comput. Biol. Chem. 2007, 31:265-274.
    • (2007) Comput. Biol. Chem. , vol.31 , pp. 265-274
    • Song, J.J.1    Lee, H.-J.2    Morris, J.S.3    Kang, S.4
  • 80
    • 33750414249 scopus 로고    scopus 로고
    • A multivariate empirical Bayes statistic for replicated microarray time course data
    • Tai Y.C., Speed T.P. A multivariate empirical Bayes statistic for replicated microarray time course data. Ann. Stat. 2006, 34:2387-2412.
    • (2006) Ann. Stat. , vol.34 , pp. 2387-2412
    • Tai, Y.C.1    Speed, T.P.2
  • 82
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher V., Tibshirani R., Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. 2001, 98:5116-5121.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 5116-5121
    • Tusher, V.1    Tibshirani, R.2    Chu, G.3
  • 85
    • 0034782618 scopus 로고    scopus 로고
    • Model-based clustering and data transformations for gene expression data
    • Yeung K.Y., Fraley C., Murua A., Raftery A.E., Ruzzo W.L. Model-based clustering and data transformations for gene expression data. Bioinformatics 2001, 17:977-987.
    • (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
  • 86
    • 1842559837 scopus 로고    scopus 로고
    • Dominant spectral component analysis for transcriptional regulations using microarray time-series data
    • Yeung L.K., Szeto L.K., Liew A.W.-C., Yan H. Dominant spectral component analysis for transcriptional regulations using microarray time-series data. Bioinformatics 2004, 20:742-749.
    • (2004) Bioinformatics , vol.20 , pp. 742-749
    • Yeung, L.K.1    Szeto, L.K.2    Liew, A.W.-C.3    Yan, H.4
  • 87
    • 0035826942 scopus 로고    scopus 로고
    • Statistical modeling of large microarray data sets to identify stimulus-response profiles
    • Zhao L.P., Prentice R., Breeden L. Statistical modeling of large microarray data sets to identify stimulus-response profiles. Proc. Natl. Acad. Sci. 2001, 98:5631-5636.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 5631-5636
    • Zhao, L.P.1    Prentice, R.2    Breeden, L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.