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Clustering Microarray Expression Data
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Bioinformatics§The application of computer science to the study of biological problems.
Clustering§Dividing the elements of a set into related subsets based on a distance metric among elements.
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Question§What other biological problem groups elements based on their "distance"?
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Reviews
	Patrik D'Haeseleer !hhttp://www.cs.unm.edu/~patrik/
	Doctoral Thesis!
	Bioinformatics article
		PMID: 11099257
		!hhttp://www.cs.unm.edu/~patrik/networks/Bioinforev.pdf
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Distance Metrics I
	Euclidean distance
	Mutual information
	Coeficient of correlation
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Distance Metrics II§Euclidean distance: distance according to Euclid's formula for geometric distance.
	Distance between points in n-dimensional space
	!i3d.png
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Common clustering techniques
	Hierarchical - Eisen et al
	K Means, Fuzzy K Means
	Self Organizing Maps (SOM) - GENECLUSTER
	Support Vector Machines (SVM)
	clique graphs - Amir Ben-Dor
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Exercise§Use a phylogeny program (like neighbor in phylip) to group the sample data.
	Phylip homepage !hhttp://evolution.genetics.washington.edu/phylip.html
	The sample !lexpr.txt  !lexpr2phylip.py
	The phylip sample !linfile  !loutfile
	What elements are most related?
	What groupings of elements stand out?
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CLUSTER
	Eisen et al PNAS !hhttp://rana.lbl.gov/papers/Eisen_PNAS_1998.pdf
	!hhttp://rana.lbl.gov/
	Free software and manuals (registration required)
	Question: what clustering technique and distance function?
:: ---
GENECLUSTER
	Tamayo et al PNAS !hhttp://www.pnas.org/cgi/content/abstract/96/6/2907
	MIT Molecular Pattern Recognition site !hhttp://www-genome.wi.mit.edu/MPR/
	Free software and manuals (registration required).
	     Tutorial at !hhttp://www-genome.wi.mit.edu/MPR/GeneCluster/GeneCluster2.html
	Question: what clustering technique and distance function?
:: --- 
GENECLUSTER clustering technique
	Self Organizing Maps
		!hhttp://www-genome.wi.mit.edu/MPR/SOM.html