Microarray Data Analysis Using BRB-ArrayTools Version 4.2.0 ...

Gene set ExpressionComparison• Allows users to find significant sets of genes rather than just significantgenes.• For the Gene Ontology comparison, , all Gene Ontology classes thatare represented in the data are tested for significance.• For Pathway Comparison, , all the pathways that are represented in thedata are tested. For Human, the BioCarta or KEGG pathways are testedand for mouse, the BioCarta pathways are compared. Additionally,Broad/MIT pathways can be downloaded to be used in analyses.• For the User Gene Lists comparison, , the user can select specificgenelists that the user would like to test for significance.• Transcription factor target gene lists and microRNA target genelistshave been added to the Gene List comparison tool.• New to v3.8, the ability to handle multiple probe sets that correspondto the same gene either using the average intensity (single channel nel dataonly) or inter quartile range.93