Modules associated with HT are enriched for ESC-like gene expression signatures. In a sample (column), each module (row) is represented by the mean expression of its component genes (“metagene”). (A) PAM was used to compare FL-pt with DLBCL-t, and modules were ordered by significance, according to their PAM score. Also shown for comparison are the FL-nt samples. There is no coherent differential expression of these modules between transforming and nontransforming FL. (B) Selected associations between transformation-related modules learned from expression data and predefined gene sets as determined by hypergeometric test with permutation correction for multiple hypothesis testing (supplemental Tables 1,4). Except for module 3, FDR values shown here are for gene sets with cell-cycle and proliferation-related genes removed.