Figure 3

Genome wide profiling of miR-503, −103, and −494 targets. (A) mRNAs enriched in the RIP-seq following miR-503, −103, or −494 transfection are also repressed. The Y-axis denotes the cumulative fraction of all mRNA transcripts profiled for each group of mRNAs denoted by line color, and the X-axis indicates the level of repression for each mRNA transcript profiled with positive values indicating increased repression. Orange: all mRNAs; Blue: mRNAs that contain the respective 7-mer miRNA seed match in their 3′UTR; Green: mRNAs that were 1.75 fold enriched in the RIP; Purple: mRNAs that were 1.75 fold enriched in the RIP and that contain the respective 7-mer miRNA seed match in their 3′UTR. Significance estimates were calculated with Student’s t-test. (B) mRNAs enriched in the RIPs had the highest frequency of the respective miRNA seed matches. The X-axis denotes consecutive groups of 250 genes, ranked from most enriched to least enriched in the RIP-seq. (C) For miR-103, and −494, mRNAs repressed in the gene expression experiments had the highest frequency of the respective miRNA seed matches. The X-axis indicates consecutive groups of 250 genes, ranked from most repressed to least repressed. (D) The highest ranked miRNA targets had the highest frequency of the respective miRNA seed matches. RIP enrichment and gene expression repression data were combined to rank miRNA targets. The X-axis denotes consecutive groups of 250 genes, from most highly ranked to least highly ranked. For B, C, and D, The line is the frequency indicated on the Y-axis of the respective 7-mer miRNA seed in the gene group compared to the frequency of the seed in all genes profiled. For B, C, and D, n = 3. E combines gene expression data, n = 3, with RIP-seq data, n = 3.