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Figure 7 | Genome Biology

Figure 7

From: Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells

Figure 7

Enrichment of RBP binding sites in PGC transcripts. (a) Enrichment of SREs evaluated by comparing the percentage of the transcripts having at least one SRE (that is, CNGGN(0-3) loop sequence with a four base pair stem) in the specific transcript category, relative to the background set (that is, all transcripts expressed at the same time point). Significance of enrichment was assessed by Bonferroni-corrected hypergeometric P-values. (b) Enrichment of SREs tested by comparing accessibility and the presence of CNGG in the specific category (that is, the positive set) versus the control category (that is, the negative set, which contained the transcripts expressed at the same time point but without any change in the expression level). Area under the receiver operator characteristic (AUROC) and Bonferroni-corrected Wilcoxon-Mann-Whitney rank sum P-values were used to represent the enrichment results and the significance level. AUROC equal to 0.5 (the dashed line), larger than 0.5 or smaller than 0.5 separately indicate that the binding site is represented equal to, more, or less in the positive set versus the negative set. (c, d) Graphs similar to (b), but representing the enrichment results for the Pumilio-binding-site (c) and AU-rich element (ARE) (d). Results that pass the significance test are shown with filled bars (multiple-test-corrected P-value ≤0.05) and the non-significant results as unfilled empty bars (multiple-test-corrected P-value > 0.05). Decay or transcription ('trans.') at the 3-to-5 hour time point relative to 1-to-3 (I) or at the 5-to-7 hour time point relative to 3-to-5 (II). smg, smaug mutant.

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