Identification of candidate functional miR-125a targets. (A) Visualization of expression of all quality-filtered predicted miR-cluster and miR-155 targets in miR-cluster–transduced and miR-155–transduced cells. Shown are MvA plots comparing 2 samples. The log2 ratio of each probe (expression difference) is plotted versus the log2 mean for each probe. The red lines represent the best fit to the data. In these plots, the predicted targets that are shared between the miR-cluster and miR-155 are not displayed. (B) Venn diagram showing the identified candidate miR-125a targets down-regulated upon miR-cluster 99b/let-7e/125a or miR-125a overexpression. The intersection represents 40 genes that were consistently 1.5-fold down-regulated upon miR-cluster 99b/let-7e/125a and miR-125a overexpression. These 40 genes were assigned according to Gene Ontology (GO) biological process categories. Genes assigned to common GO categories were grouped together (supplemental Table 3). The pie chart shows relative distributions of grouped GO categories. The size of the sectors in the pie chart was defined based on the number of genes assigned to the category (in redundant fashion). Genes not assigned to any of the defined categories^1–7  were defined as Other.⁸  Gene Ontology analyses were performed using GOAL software.⁴⁰