Figure 4. Genes associated with the proliferative state of tumors are cell cycle regulated. A. Cell cycle regulation of the breast tumor proliferation cluster. The expression patterns of the 112 clones in the breast tumor "proliferation cluster" (Perou et al., 2000), were examined in the cell cycle dataset, along with their expression in breast tumors and cell lines. The clones are ordered by their peak expression during the cell cycle (as in Figure 3A) such that each row corresponds to a single clone. The order of the breast tumor samples based on hierarchical clustering using 1753 genes is as previously described (Perou et al., 2000). The mitotic grade of the tumors is indicated (a higher mitotic grade is indicative of a more proliferative tumor). Of the 112 genes in the proliferation cluster, 74 were identified as cell cycle regulated in this study. B. Cell cycle regulation of lymphoma proliferation cluster. Since the lymphoma study was performed on the Lymphochip Microarray, which is comprised of a different clone set than the Stanford Human Microarray used for this study, the genes on the two arrays were linked together via their LocusLink ID (Pruitt and Maglott, 2001). 154 clones were selected from the previously published lymphoma proliferation cluster (Alizadeh et al., 2000) and 19 clones without LocusLink IDs were discarded. Of the remaining 135, 128 clones with matching LocusLink IDs were measured in our cell cycle study. Duplicate clones were removed leaving 96 genes. Of these, 43 were identified as cell cycle regulated in this study. As above, the genes (i.e. rows) are ordered by peak expression during the cell cycle. The order of the tumors, based on hierarchical clustering using a larger dataset, is as previously published (Alizadeh et al., 2000). This figure with all gene names is available as supplemental Figure 10.