SAM and pathway analysis of a dataset normalized with and without lung NEPS genes. (A) Number of probes identified as differentially over and underexpressed between cancer and normal using SAM on the dataset with and without NEPS normalization. Venn diagram illustrates the overlap in the genes identified as well as those which are different between the two analyses. (B) Canonical pathway analysis using Ingenuity Pathway Analysis. Dark blue bars represent the results from the dataset normalized with MAS 5.0 + NEPS and light blue bars represent the results from normalization using MAS 5.0 alone. The pathways which are the most significant are the most significant in both analyses. Note that key pathways such as Neuregulin signaling and JAK/Stat are identified with higher significance when normalized using the lung NEPS genes. Such differences illustrate the impact of reference gene selection and normalization on differential gene expression analysis.