Through the genome-wide characterization of a cell type’s transcriptome, gene expression profile analysis provides a potent tool for analyzing the pathogenesis of lymphomas and has had a major impact on the understanding of lymphoid neoplasia. The analysis of gene expression patterns of lymphomas and normal lymphocytes permits (1) the definition of molecular subtypes of lymphoma; (2) the identification of the normal cellular counterpart of a lymphoma subtype; (3) the identification of diagnostic markers and therapeutic targets; and (4) the identification of signaling pathways affected by the oncogenic transformation. This chapter presents an approach to accomplish these goals.
