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한국통계학회 논문집 = Communications of the Korean Statistical Society, v.11 no.1, 2004년, pp.59 - 77
Kim, Choongrak (Department of Statistics, Pusan National University)
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Since the introduction of DNA microarray, a revolutionary high through-put biological technology, a lot of papers have been published to deal with the analyses of the gene expression data from the microarray. In this paper we review most papers relevant to the cDNA microarray data, classify them in ...
Alizadeh, Ash A., Eisen, Michael B., Davis, R. Eric, Ma, Chi, Lossos, Izidore S., Rosenwald, Andreas, Boldrick, Jennifer C., Sabet, Hajeer, Tran, Truc, Yu, Xin, Powell, John I., Yang, Liming, Marti, Gerald E., Moore, Troy, Hudson Jr, James, Lu, Lisheng, Lewis, David B., Tibshirani, Robert, Sherlock, Gavin, Chan, Wing C., Greiner, Timothy C., Weisenburger, Dennis D., Armitage, James O., Warnke, Roger, Levy, Ronald, Wilson, Wyndham, Grever, Michael R., Byrd, John C., Botstein, David, Brown, Patrick O., Staudt, Louis M.. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, vol.403, no.6769, 503-511.
10.1073/pnas.97.18.10101
Bassett Jr, Douglas E., Eisen, Michael B., Boguski, Mark S.. Gene expression informatics -it's all in your mine. Nature genetics, vol.21, no.1, 51-55.
Ben-Dor, Amir, Bruhn, Laurakay, Friedman, Nir, Nachman, Iftach, Schummer, Michèl, Yakhini, Zohar. Tissue Classification with Gene Expression Profiles. Journal of computational biology : a journal of computational molecular cell biology, vol.7, no.3, 559-583.
Benito, Monica, Parker, Joel, Du, Quan, Wu, Junyuan, Xiang, Dong, Perou, Charles M., Marron, J. S.. Adjustment of systematic microarray data biases. Bioinformatics, vol.20, no.1, 105-114.
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Chen, Y, Dougherty, E R, Bittner, M L. Ratio-based decisions and the quantitative analysis of cDNA microarray images.. Journal of biomedical optics, vol.2, no.4, 364-374.
Chen, Yidong, Kamat, Vishnu, Dougherty, Edward R., Bittner, Michael L., Meltzer, Paul S., Trent, Jeffery M.. Ratio statistics of gene expression levels and applications to microarray data analysis. Bioinformatics, vol.18, no.9, 1207-1215.
Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P. O., Herskowitz, I.. The Transcriptional Program of Sporulation in Budding Yeast. Science, vol.282, no.5389, 699-705.
Coombes, Kevin R., Highsmith, W. Edward, Krogmann, Tammy A., Baggerly, Keith A., Stivers, David N., Abruzzo, Lynne V.. Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays. Journal of computational biology : a journal of computational molecular cell biology, vol.9, no.4, 655-669.
Dettling, Marcel, Bühlmann, Peter. Boosting for tumor classification with gene expression data. Bioinformatics, vol.19, no.9, 1061-1069.
Ding, Chris H.Q.. Unsupervised feature selection via two-way ordering in gene expression analysis. Bioinformatics, vol.19, no.10, 1259-1266.
Dougherty, Edward R., Barrera, Junior, Brun, Marcel, Kim, Seungchan, Cesar, Roberto M., Chen, Yidong, Bittner, Michael, Trent, Jeffrey M.. Inference from Clustering with Application to Gene-Expression Microarrays. Journal of computational biology : a journal of computational molecular cell biology, vol.9, no.1, 105-126.
Duggan, David J, Bittner, Michael, Chen, Yidong, Meltzer, Paul, Trent, Jeffrey M.. Expression profiling using cDNA microarrays. Nature genetics, vol.21, no.1, 10-14.
Dudoit, Sandrine, Fridlyand, Jane, Speed, Terence P. Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data. Journal of the American Statistical Association, vol.97, no.457, 77-87.
Dudoit, Sandrine, Fridlyand, Jane. Bagging to improve the accuracy of a clustering procedure. Bioinformatics, vol.19, no.9, 1090-1099.
Edwards, David. Non-linear normalization and background correction in one-channel cDNA microarray studies. Bioinformatics, vol.19, no.7, 825-833.
Efron, B., Tibshirani, R., Storey, J. D., Tusher, V.. Empirical Bayes Analysis of a Microarray Experiment. Journal of the American Statistical Association, vol.96, no.456, 1151-1160.
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Freund, Y., Schapire, R.E.. A Decision-Theoretic Generalization of On-Line Learning and an Application to Boosting. Journal of computer and system sciences, vol.55, no.1, 119-139.
Genovese, Christopher, Wasserman, Larry. Operating Characteristics and Extensions of the False Discovery Rate Procedure. Journal of the Royal Statistical Society Series B, Statistical methodology, vol.64, no.3, 499-517.
Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., Bloomfield, C. D., Lander, E. S.. Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. Science, vol.286, no.5439, 531-537.
Goryachev, Andrew B., Macgregor, Pascale F., Edwards, Aled M.. Unfolding of Microarray Data. Journal of computational biology : a journal of computational molecular cell biology, vol.8, no.4, 443-461.
Genome Biology 2 1 2001
Holter, Neal S., Mitra, Madhusmita, Maritan, Amos, Cieplak, Marek, Banavar, Jayanth R., Fedoroff, Nina V.. Fundamental patterns underlying gene expression profiles: Simplicity from complexity. Proceedings of the National Academy of Sciences of the United States of America, vol.97, no.15, 8409-8414.
Holter, Neal S., Maritan, Amos, Cieplak, Marek, Fedoroff, Nina V., Banavar, Jayanth R.. Dynamic modeling of gene expression data. Proceedings of the National Academy of Sciences of the United States of America, vol.98, no.4, 1693-1698.
Ibrahim, J. G., Chen, M.-H., Gray, R. J.. Bayesian Models for Gene Expression With DNA Microarray Data. Journal of the American Statistical Association, vol.97, no.457, 88-99.
Kerr, M. Kathleen, Martin, Mitchell, Churchill, Gary A.. Analysis of Variance for Gene Expression Microarray Data. Journal of computational biology : a journal of computational molecular cell biology, vol.7, no.6, 819-837.
Kerr, M. Kathleen, Churchill, Gary A.. Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments. Proceedings of the National Academy of Sciences of the United States of America, vol.98, no.16, 8961-8965.
Kooperberg, Charles, Fazzio, Thomas G., Delrow, Jeffrey J., Tsukiyama, Toshio. Improved Background Correction for Spotted DNA Microarrays. Journal of computational biology : a journal of computational molecular cell biology, vol.9, no.1, 55-66.
Statistica Sinica 12 61 2002
10.1073/pnas.97.18.9834
Lee, Yoonkyung, Lee, Cheol-Koo. Classification of multiple cancer types by multicategory support vector machines using gene expression data. Bioinformatics, vol.19, no.9, 1132-1139.
Lockhart, David J., Dong, Helin, Byrne, Michael C., Follettie, Maximillian T., Gallo, Michael V., Chee, Mark S., Mittmann, Michael, Wang, Chunwei, Kobayashi, Michiko, Norton, Heidi, Brown, Eugene L.. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature biotechnology, vol.14, no.13, 1675-1680.
Statistica Sinica 12 31 2002
Jourma of Computational Biology 8 37 2000
Nguyen, Danh V., Bulak Arpat, A., Wang, Naisyin, Carroll, Raymond J.. DNA Microarray Experiments: Biological and Technological Aspects. Biometrics, vol.58, no.4, 701-717.
Olshen, Adam B., Jain, Ajay N.. Deriving quantitative conclusions from microarray expression data. Bioinformatics, vol.18, no.7, 961-970.
Radmacher, Michael D., McShane, Lisa M., Simon, Richard. A Paradigm for Class Prediction Using Gene Expression Profiles. Journal of computational biology : a journal of computational molecular cell biology, vol.9, no.3, 505-511.
Reiner, Anat, Yekutieli, Daniel, Benjamini, Yoav. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics, vol.19, no.3, 368-375.
Ross, Douglas T., Scherf, Uwe, Eisen, Michael B., Perou, Charles M., Rees, Christian, Spellman, Paul, Iyer, Vishwanath, Jeffrey, Stefanie S., Van de Rijn, Matt, Waltham, Mark, Pergamenschikov, Alexander, Lee, Jeffrey C.F., Lashkari, Deval, Shalon, Dari, Myers, Timothy G., Weinstein, John N., Botstein, David, Brown, Patrick O.. Systematic variation in gene expression patterns in human cancer cell lines. Nature genetics, vol.24, no.3, 227-235.
10.1002/1097-4644(20010201)80:2<192::AID-JCB50>3.0.CO;2-W
Schadt, Eric E., Li, Cheng, Ellis, Byron, Wong, Wing H.. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. Journal of cellular biochemistry, vol.84, no.suppl37, 120-125.
Schena, Mark, Shalon, Dari, Davis, Ronald W., Brown, Patrick O.. Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray. Science, vol.270, no.5235, 467-470.
Scherf, Uwe, Ross, Douglas T., Waltham, Mark, Smith, Lawrence H., Lee, Jae K., Tanabe, Lorraine, Kohn, Kurt W., Reinhold, William C., Myers, Timothy G., Andrews, Darren T., Scudiero, Dominic A., Eisen, Michael B., Sausville, Edward A., Pommier, Yves, Botstein, David, Brown, Patrick O., Weinstein, John N.. A gene expression database for the molecular pharmacology of cancer. Nature genetics, vol.24, no.3, 236-244.
Sebastiani, Paola, Gussoni, Emanuela, Kohane, Isaac S., Ramoni, Marco F.. Statistical Challenges in Functional Genomics. Statistical science : a review journal of the Institute of Mathematical Statistics, vol.18, no.1,
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Storey, John D.. A Direct Approach to False Discovery Rates. Journal of the Royal Statistical Society Series B, Statistical methodology, vol.64, no.3, 479-498.
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Tibshirani, Robert, Hastie, Trevor, Narasimhan, Balasubramanian, Chu, Gilbert. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proceedings of the National Academy of Sciences of the United States of America, vol.99, no.10, 6567-6572.
Tseng, George C., Oh, Min-Kyu, Rohlin, Lars, Liao, James C., Wong, Wing Hung. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic acids research, vol.29, no.12, 2549-2557.
Tusher, Virginia Goss, Tibshirani, Robert, Chu, Gilbert. Significance analysis of microarrays applied to the ionizing radiation response. Proceedings of the National Academy of Sciences of the United States of America, vol.98, no.9, 5116-5121.
Wang, Song, Ethier, Stewart. A generalized likelihood ratio test to identify differentially expressed genes from microarray data. Bioinformatics, vol.20, no.1, 100-104.
Wilson, D.L., Buckley, M.J., Helliwell, C.A., Wilson, I.W.. New normalization methods for cDNA microarray data. Bioinformatics, vol.19, no.11, 1325-1332.
Wolfinger, Russell D., Gibson, Greg, Wolfinger, Elizabeth D., Bennett, Lee, Hamadeh, Hisham, Bushel, Pierre, Afshari, Cynthia, Paules, Richard S.. Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models. Journal of computational biology : a journal of computational molecular cell biology, vol.8, no.6, 625-637.
Yang, Y. H., Buckley, M. J., Dudoit, S., Speed, T. P.. Comparison of Methods for Image Analysis on cDNA Microarray Data. Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America, vol.11, no.1, 108-136.
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