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. Author manuscript; available in PMC: 2011 Aug 1.
Published in final edited form as: Nat Struct Mol Biol. 2011 Jan 23;18(2):237–244. doi: 10.1038/nsmb.1991

Figure 2. Ago2-CLIP genes exhibit a miRNA-dependent gene expression signature.

Figure 2

(a, c, e, f) CDFs (cumulative density functions) of the log2 fold change (LFC) in mRNA expression between the wild-type (WT) and Dicer−/− (KO) mESCs. Fold change is ratio of expression level in WT cells to expression level in KO cells, such that a CDF with a more negative LFC compared to another CDF indicates that the distribution has lower mRNA expression in wild-type mESCs relative to Dicer−/− mESCs (i.e. population includes mRNAs that are more downregulated in presence of miRNAs). Refer to Supplementary Table 4 for detailed descriptions on statistics and Supplementary Table 5 for gene lists. (b, d) Box plots of branch lengths (top), i.e. “Conservation”, and “Context” scores (bottom) computed by TargetScan 5.1. (a-d) Gene sets include: Ago2-CLIP 3′ UTR GCACUU-motif mRNAs (blue) that passed the Normalization and Multi-Library filters (a-b, “Overlap”) or just the Normalization filter (c-d, “All”) in any WT library; “Conserved predicted” expression-matched TargetScan GCACUU targets (dark pink), ranked by branch length (i.e. conservation), then by context score (a, Top-ranked 43 genes; c, Top-ranked 201 genes); “All predicted” expression-matched TargetScan GCACUU targets (light pink, 1469 genes); and “Control” mRNAs (grey). (e) Gene sets include: Ago2-CLIP CDS GCACUU-containing mRNAs that passed the Normalization filter in any WT library (“CLIP”, blue), “Predicted” GCACUU-containing CDS mRNAs (pink) that were expression-matched to the “CLIP” set but lacked GCACUU in their 3′UTRs, and matched “control” mRNAs (grey). (f) Gene sets include: Ago2-CLIP 3′ UTR GCACUU-containing (blue) and G-motif-containing mRNAs (red) that passed the Normalization and Multi-Library filters in WT libraries, Ago2-CLIP 3′UTR CCAGCC-containing mRNAs (orange) that passed the Normalization filter in at least one WT library, and corresponding matched controls (grey). Any mRNAs with GCACUU in the 3′UTR or CDS were removed from the “G-motif” and “CCAGCC” sets. Error bar is SD.