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