Table 2.

Current data analysis and display modules

Method Name	Reference	Method Description
Simple Count	FACT	Count and display of occurrences of annotation terms
GO-Term Comparison	In part from GO::TermFinder [15]	Detection of significantly overrepresented GO terms in Gene List, based upon hypergeometric tail probability
MedLiner	Bio::Biblio (M. Senger, EBI)	List Publications with co-occurrences of terms
CGH database	Deutsches Krebsforschungs-zentrum, Div. Molecular Genetics (D)	Compare CGH results to archived data
goCluster	goCluster, G. Wrobel, available at http://www.bioconductor.org	Detection of significantly overrepresented GO terms (based upon Fisher's exact test) in Clusters built with k-means algorithm
Hypergeometric Tail	In part from GeneMerge [14]	Detection of significantly overrepresented terms of any kind, based upon hypergeometric tail probability
CGH – Expression Comparison	FACT	Detect correlation between genomic and expression data sets, based on two-sided T-Tests
Chromosomal Plot	FACT	Display values or occurrences in genomic context