8 showed Asunaprevir price significantly higher intensity in ER2 tumors . All probe sets for E2F1 and E2F5 and one probe set for E2F4 had higher intensity in ER2 tumors, but did not pass the adjusted P significance threshold. Probe sets for TFDP1 and TFDP2, members of the DP transcription factor family, whose products form heterodimers with E2Fs 1 to 6 producing transcription factor complexes that bind to DNA, were significantly higher in ER2 tumors. One probe set for p130, a pocket protein that binds principally to E2Fs 4 and 5 converting them into repressor complexes, had significantly lower intensity in ER2 tumors with the other probe set showing the same trend. For each gene above, the tWAR, indicating fold-change, was small, with the possible exception of the two probe sets for E2F3. In the GSEA screen, several gene sets significantly enriched in ER2 tumors were associated with E2F activity. Nineteen sets contained genes with 22315414 conserved DNA binding motifs for E2F family members, particularly E2F1 and E2F4. Different members of the E2F family can bind to the same genes depending on the conditions such as the phase of the cell cycle, and these motif sets had many genes in common. Supporting the observations for genes with conserved E2F motifs, a MolSigDB list of genes up-regulated by E2Fs 1, 2 or 3 and down-regulated by pRB and p16INK4A in U2OS cells was enriched in ER2 tumors . The complementary set of genes down-regulated by E2Fs 1, 2 or 3 and up-regulated by pRB and p16INK4A was depleted. In order to better understand the roles E2Fs might play in the regulation of proliferation in ER2 tumors, we included additional published sets of direct targets of E2Fs 1, 4 and 6, as well as sets of genes regulated by E2F1 or E2F3. A list of genes regulated by E2F1 in mouse embryonic fibroblasts was enriched with FDR,0.0001, as was a set of genes regulated by E2F3 from the same study. Several sets of direct targets of E2F1 and E2F4 were significantly enriched in ER2 tumors. The sets enriched with FDR,0.0001 included direct targets of E2F4 in MEFs during either G0 or early G1 stage of the cell cycle, genes bound by both E2F4 and E2F1 in WI-38 primary human fibroblast cells, and genes bound by E2F4 and not E2F1 in the same study. The pocket proteins p130 and p107 bind to E2F4 converting it 19478133 to a repressor complex, and consistent with this association, direct targets of p130 in MEFs during G0 or G1 were enriched with FDR,0.0001, 
as were targets of p107 during G1. To examine if the enrichment of E2F activity differed between the subtypes of ER2 tumors, we clustered the validation tumor datasets using ERA genes that were associated with E2F activity. We confirmed that the enriched set of direct targets of E2F4 in MEFs had higher expression in samples with low levels of ER. These genes had particularly high expression in the basal subgroup compared to the ER2/ERBB2+ subgroup in all three datasets,. The ERA genes MYC and E2F 9 MYC and E2F overlapping with sets of genes activated by E2Fs 1, 2 or 3 in U2OS cells, by E2F1 or E2F3 in MEFs and all the enriched gene sets of direct targets of E2Fs 1, 4 or 6 also showed differential expression in the basal tumors. ERA genes that were direct targets of E2F4 and over-expressed in basal ER2 tumors were also over-expressed with respect to normal tissue,. To ascertain if the enrichment noted for the MYC and E2F sets was entirely due to the presence of proliferation-associated genes in these sets, we removed genes in the GO cell cycle
