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Given the large number of genes recorded in microarray experiments, gene expression data are generally displayed on a low dimensional plot, based on linear methods. However, microarray data show nonlinearity, due to high-order terms of interaction between genes, so alternative approaches, such as kernel methods, may be more appropriate. We introduce a technique that combines kernel principal component analysis (KPCA) and Biplot to visualize gene expression profiles. Our approach relies on the singular value decomposition of the input matrix and incorporates an additional step that involves KPCA. The main properties of our method are the extraction of nonlinear features and the preservation of the input variables (genes) in the output display. We apply this algorithm to colon tumor, leukemia and lymphoma datasets. Our approach reveals the underlying structure of the gene expression profiles and provides a more intuitive understanding of the gene and sample association.<\/jats:p>","DOI":"10.1016\/s1672-0229(10)60022-8","type":"journal-article","created":{"date-parts":[[2010,10,22]],"date-time":"2010-10-22T11:07:03Z","timestamp":1287745623000},"page":"200-210","source":"Crossref","is-referenced-by-count":15,"title":["Mining Gene Expression Profiles: An Integrated Implementation of Kernel Principal Component Analysis and Singular Value Decomposition"],"prefix":"10.1093","volume":"8","author":[{"given":"Ferran","family":"Reverter","sequence":"first","affiliation":[{"name":"Department of Statistics, Faculty of Biology, University of Barcelona , 08028 Barcelona , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Esteban","family":"Vegas","sequence":"additional","affiliation":[{"name":"Department of Statistics, Faculty of Biology, University of Barcelona , 08028 Barcelona , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pedro","family":"S\u00e1nchez","sequence":"additional","affiliation":[{"name":"Department of Statistics, Faculty of Biology, University of Barcelona , 08028 Barcelona , Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,10,21]]},"reference":[{"key":"2024051409230074700_bib1","volume-title":"Graphical Methods for Data Analysis","author":"Chambers","year":"1983"},{"key":"2024051409230074700_bib2","doi-asserted-by":"crossref","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","article-title":"Cluster analysis and display of genome-wide expression patterns","volume":"95","author":"Eisen","year":"1998","journal-title":"Proc. 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