{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T16:25:56Z","timestamp":1774628756971,"version":"3.50.1"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2001,6,1]],"date-time":"2001-06-01T00:00:00Z","timestamp":991353600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nat Rev Genet"],"published-print":{"date-parts":[[2001,6]]},"DOI":"10.1038\/35076576","type":"journal-article","created":{"date-parts":[[2002,9,20]],"date-time":"2002-09-20T20:02:07Z","timestamp":1032552127000},"page":"418-427","source":"Crossref","is-referenced-by-count":1061,"title":["Computational analysis of microarray data"],"prefix":"10.1038","volume":"2","author":[{"given":"John","family":"Quackenbush","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"BF35076576_CR1","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1126\/science.270.5235.484","volume":"270","author":"VE Velculescu","year":"1995","unstructured":"Velculescu, V. E., Zhang, L., Vogelstein, B. & Kinzler, K. W. Serial analysis of gene expression. Science 270, 484\u2013487 (1995).","journal-title":"Science"},{"key":"BF35076576_CR2","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.1038\/nbt1296-1675","volume":"14","author":"DJ Lockhart","year":"1996","unstructured":"Lockhart, D. J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675\u20131680 (1996).","journal-title":"Nature Biotechnol."},{"key":"BF35076576_CR3","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1126\/science.270.5235.467","volume":"270","author":"M Schena","year":"1995","unstructured":"Schena, M., Shalon, D., Davis, R. W. & Brown, P. O. Quantitative monitoring of gene expression patterns with complementary DNA microarray. Science 270, 467\u2013470 (1995).","journal-title":"Science"},{"key":"BF35076576_CR4","doi-asserted-by":"publisher","first-page":"10614","DOI":"10.1073\/pnas.93.20.10614","volume":"93","author":"M Schena","year":"1996","unstructured":"Schena, M. et al. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl Acad. Sci. USA 93, 10614\u201310619 (1996).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BF35076576_CR5","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1073\/pnas.95.1.334","volume":"95","author":"X Wen","year":"1998","unstructured":"Wen, X. et al. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl Acad. Sci. USA 95, 334\u2013339 (1998).This is one of the first analyses of large-scale gene expression \u2014 in this case, RT\u2013PCR data \u2014 using clustering and data-mining techniques. It elegantly shows how integrating the results derived using various distance metrics can reveal different but meaningful patterns in the data.","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BF35076576_CR6","first-page":"42","volume":"1998","author":"GS Michaels","year":"1998","unstructured":"Michaels, G. S. et al. Cluster analysis and data visualization of large-scale gene expression data. Pacific Symp. Biocomput. 1998, 42\u201353 (1998).","journal-title":"Pacific Symp. Biocomput."},{"key":"BF35076576_CR7","doi-asserted-by":"publisher","first-page":"14863","DOI":"10.1073\/pnas.95.25.14863","volume":"95","author":"MB Eisen","year":"1998","unstructured":"Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863\u201314868 (1998).This is an excellent demonstration of the power of hierarchical clustering to the analysis of microarray data. The authors also provide software \u2014 Cluster and Treeview \u2014 which became the standard for analysing microarray data.","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BF35076576_CR8","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1126\/science.275.5298.343","volume":"275","author":"JN Weinstein","year":"1997","unstructured":"Weinstein, J. N. et al. An information-intensive approach to the molecular pharmacology of cancer. Science 275, 343\u2013349 (1997).Weinstein and colleagues present one of the first and most elegant applications of hierarchical clustering and other data-mining and visualization techniques to the analysis of large-scale data in molecular biology.","journal-title":"Science"},{"key":"BF35076576_CR9","first-page":"1409","volume":"38","author":"RR Sokal","year":"1958","unstructured":"Sokal, R. R. & Michener, C. D. A statistical method for evaluating systematic relationships. Univ. Kans. Sci. Bull. 38, 1409\u20131438 (1958).","journal-title":"Univ. Kans. Sci. Bull."},{"key":"BF35076576_CR10","volume-title":"The Mathematical Theory of Communication","author":"CC Shannon","year":"1963","unstructured":"Shannon, C. C. & Weaver, W. The Mathematical Theory of Communication (Illinois Univ. Press, Illinois, 1963)."},{"key":"BF35076576_CR11","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-642-97610-0","volume-title":"Self Organizing Maps","author":"T Kohonen","year":"1995","unstructured":"Kohonen, T. Self Organizing Maps (Springer, Berlin, 1995)."},{"key":"BF35076576_CR12","doi-asserted-by":"publisher","first-page":"2907","DOI":"10.1073\/pnas.96.6.2907","volume":"96","author":"P Tamayo","year":"1999","unstructured":"Tamayo, P. et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA 96, 2907\u20132912 (1999).Tamayo and colleagues use self-organizing maps (SOMs) to explore patterns of gene expression generated using Affymetrix arrays, and provide the GENECLUSTER implementation of SOMs.","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BF35076576_CR13","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1016\/S0076-6879(99)03014-1","volume":"303","author":"MB Eisen","year":"1999","unstructured":"Eisen, M. B. & Brown, P. O. DNA arrays for analysis of gene expression. Meth. Enzymol. 303, 179\u2013205 (1999).","journal-title":"Meth. Enzymol."},{"key":"BF35076576_CR14","doi-asserted-by":"publisher","first-page":"548","DOI":"10.2144\/00293bi01","volume":"29","author":"P Hegde","year":"2000","unstructured":"Hegde, P. et al. A concise guide to microarray analysis. Biotechniques 29, 548\u2013560 (2000).","journal-title":"Biotechniques"},{"key":"BF35076576_CR15","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1038\/ng0895-369","volume":"10","author":"MS Boguski","year":"1995","unstructured":"Boguski, M. S. & Schuler, G. D. ESTablishing a human transcript map. Nature Genet. 10, 369\u2013371 (1995).","journal-title":"Nature Genet."},{"key":"BF35076576_CR16","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1093\/nar\/29.1.159","volume":"29","author":"J Quackenbush","year":"2001","unstructured":"Quackenbush, J. et al. The TIGR gene indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res. 29, 159\u2013164 (2001).","journal-title":"Nucleic Acids Res"},{"key":"BF35076576_CR17","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1101\/gr.8.3.276","volume":"8","author":"J Burke","year":"1998","unstructured":"Burke, J., Wang, H., Hide, W. & Davison, D. B. Alternative gene form discovery and candidate gene selection from gene indexing projects. Genome Res. 8, 276\u2013290 (1998).","journal-title":"Genome Res."},{"key":"BF35076576_CR18","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1038\/1670","volume":"20","author":"O Ermolaeva","year":"1998","unstructured":"Ermolaeva, O. et al. Data management and analysis for gene expression arrays. Nature Genet. 20, 19\u201323 (1998).","journal-title":"Nature Genet."},{"key":"BF35076576_CR19","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1093\/nar\/29.1.152","volume":"29","author":"G Sherlock","year":"2001","unstructured":"Sherlock, G. et al. The Stanford Microarray Database. Nucleic Acids Res. 29, 152\u2013155 (2001).","journal-title":"Nucleic Acids Res."},{"key":"BF35076576_CR20","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1117\/12.281504","volume":"2","author":"Y Chen","year":"1997","unstructured":"Chen, Y., Dougherty, E. R. & Bittner, M. Ratio-based decisions and the quantitative analysis of cDNA microarray images. J. Biomed. Opt. 2, 364\u2013374 (1997).","journal-title":"J. Biomed. Opt."},{"key":"BF35076576_CR21","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1101\/gr.9.11.1106","volume":"9","author":"LJ Heyer","year":"1999","unstructured":"Heyer, L. J., Kruglyak, L. & Yooseph, S. Exploring expression data: identification and analysis of coexpressed genes. Genome Res. 9, 1106\u20131115 (1999).","journal-title":"Genome Res."},{"key":"BF35076576_CR22","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1038\/10343","volume":"22","author":"S Tavazoie","year":"1999","unstructured":"Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J. & Church, G. M. Systematic determination of genetic network architecture. Nature Genet. 22, 281\u2013285 (1999).","journal-title":"Nature Genet."},{"key":"BF35076576_CR23","first-page":"455","volume":"2000","author":"S Raychaudhuri","year":"2000","unstructured":"Raychaudhuri, S., Stuart, J. M. & Altman, R. B. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac. Symp. Biocomput. 2000, 455\u2013466 (2000).","journal-title":"Pac. Symp. Biocomput."},{"key":"BF35076576_CR24","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1073\/pnas.97.1.262","volume":"97","author":"MP Brown","year":"2000","unstructured":"Brown, M. P. et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA 97, 262\u2013267 (2000).This paper shows the power of supervised techniques, in this case support vector machines, to provide additional insight into gene expression and function.","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BF35076576_CR25","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1126\/science.286.5439.531","volume":"286","author":"TR Golub","year":"1999","unstructured":"Golub, T. R. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531\u2013537 (1999).","journal-title":"Science"},{"key":"BF35076576_CR26","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1093\/bioinformatics\/16.10.906","volume":"16","author":"TS Furey","year":"2000","unstructured":"Furey, T. S. et al. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16, 906\u2013914 (2000).","journal-title":"Bioinformatics"},{"key":"BF35076576_CR27","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1056\/NEJM200102223440801","volume":"344","author":"I Hedenfalk","year":"2001","unstructured":"Hedenfalk, I. et al. Gene-expression profiles in hereditary breast cancer. N. Engl. J. Med. 344, 539\u2013548 (2001).","journal-title":"N. Engl. J. Med."},{"key":"BF35076576_CR28","volume-title":"Regression Analysis by Example","author":"S Chatterjee","year":"1991","unstructured":"Chatterjee, S. & Price, B. Regression Analysis by Example (John Wiley and Sons, New York, 1991)."},{"key":"BF35076576_CR29","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1080\/01621459.1988.10478639","volume":"83","author":"WS Cleveland","year":"1988","unstructured":"Cleveland, W. S. & Devlin, S. J. Locally weighted regression: an approach to regression analysis by local fitting. J. Am. Stat. Assoc. 83, 596\u2013610 (1988).","journal-title":"J. Am. Stat. Assoc."},{"key":"BF35076576_CR30","volume-title":"Principles of Numerical Taxonomy","author":"RR Sokal","year":"1963","unstructured":"Sokal, R. R. & Sneath, P. H. A. Principles of Numerical Taxonomy (W. H. Freeman & Co., San Francisco, 1963)."},{"key":"BF35076576_CR31","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1080\/01621459.1963.10500845","volume":"58","author":"JH Ward","year":"1963","unstructured":"Ward, J. H. Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc. 58, 236\u2013244 (1963).","journal-title":"J. Am. Stat. Assoc."}],"container-title":["Nature Reviews Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/35076576.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/35076576","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/35076576.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T01:59:01Z","timestamp":1684288741000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/35076576"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2001,6]]},"references-count":31,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2001,6]]}},"alternative-id":["BF35076576"],"URL":"https:\/\/doi.org\/10.1038\/35076576","relation":{},"ISSN":["1471-0056","1471-0064"],"issn-type":[{"value":"1471-0056","type":"print"},{"value":"1471-0064","type":"electronic"}],"subject":[],"published":{"date-parts":[[2001,6]]}}}