Significance analysis of microarrays (SAM)
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Identifies differentially expressed genes between sample sets; estimates significance for genes; considers large numbers of genes in array experiments
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[9]
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Stanford University, http://www-stat.stanford.edu/~tibs/ x-mine, Brisbane, CA, http://www.x-mine.com/
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Hierarchal clustering
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Unsupervised clustering; clusters genes with similar expression patterns; clusters samples with similar expression patterns
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[15]
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University of California, Berkeley, http://rana.lbl.gov/EisenSoftware.htm
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Supervised harvesting classification
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Class prediction; identifies subset of genes that best classify samples as gene sets; estimates accuracy of gene set on prospective population
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[10]
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x-mine, Brisbane, CA, http://www.x-mine.com/
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Classification and regression trees (CART), multiple additive regression trees (MART)
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Class prediction; develops decision trees to classify samples using the expression of a subset of genes; estimates accuracy of the gene panel on a prospective set
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[12, 14]
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CART: Salford Systems, http://www.salford-systems.com/ MART: Stanford University, http://www-stat.stanford.edu/~jhf/R-MART.html or Salford Systems
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Shrunken centroids (prediction analysis for microarrays, PAM)
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Class prediction; identifies subset of genes that best classify samples as gene sets; estimates accuracy of gene set on prospective population
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[11]
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Stanford University, http://www-stat.stanford.edu/~tibs/PAM/index.html
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Affymetrix MAS 5.0
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Affymetrix
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GeneSpring
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Silicon Genetics
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Pathways 3.0
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Research Genetics
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