Flowchart of murine expression data analysis. Agilent microarrays from three different platforms were normalized and combined together to create a single murine expression dataset. Next, an unsupervised cluster analysis using variably expressed genes was performed to define a murine ‘intrinsic gene list’. Third, this intrinsic list was used as part of a supervised cluster analysis to objectively define murine subtypes/classes. Fourth, class based supervised analyses were used to define murine class specific lists (genes and pathways). Finally, supervised comparative analysis between human subtypes and mouse classes was used to identify and characterize human-mouse counterparts. NF, normalization factor. GSA, gene set analysis; SAM, Significance Analysis of Microarrays.