Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance (original) (raw)
Figure 3
Comparison of mRNA and miRNA specifically associated with Ago2 in the absence or presence of miR-1 or miR-124.
(A) Supervised hierarchical cluster of putative Ago2 targets that are enriched over mock (local FDR 1%) from FLAG purifications of FLAG-Ago2 transfected cells (red) and mock transfected cells (blue). Rows correspond to 1,215 gene elements (representing ∼1,083 genes) and columns represent individual experimental samples. There is a high correlation between replicate experiments: rave = 0.80 for Ago2 replicates, 0.73 for mock replicates, and −0.070 for all experiments. (B) Scatter plot of the normalized log2 microarray signal intensities of 90 miRNAs from whole cell lysate (x-axis) graphed against the normalized log2 microarray signal intensities of miRNAs associated with Ago2 (y-axis, r = 0.92). Four replicates were performed for each experiment. The grey lines delineate the boundary for a two-fold change. (C) Supervised hierarchical clustering of putative miR-1 and miR-124 targets enriched over Ago2 alone (1% local FDR) from FLAG purifications of FLAG-Ago2 transfected cells alone (red) and FLAG-Ago2 transfected cells with miR-1 (green) or miR-124 (purple). Rows correspond to 667 gene features (representing ∼544 genes) and columns represent individual experimental samples. rave = 0.80 for Ago2 replicates, 0.77 for Ago2+miR-1 replicates, 0.90 for Ago2+miR-124 replicates, and 0.43 for all experiments.