Extended Data Fig. 5: Association between RBP binding and RNA expression changes upon RBP knockdown.
From: A large-scale binding and functional map of human RNA-binding proteins
a, Heatmap indicates significance of overlap between genes with regions that were significantly enriched (P ≤ 10−5 and ≥fourfold enriched in eCLIP versus input) and genes that were significantly (top) increased or (bottom) decreased (P < 0.05 and false discovery rate (FDR) < 0.05) in RBP knockdown RNA-seq experiments using DESeq analysis with no G/C content normalization (see Supplementary Methods and Supplementary Fig. 2). Significance determined by two-sided Fisher’s exact test or Yates’ χ2 approximation where appropriate; *P < 0.05, **P < 10−5 after Bonferroni correction. Shown are all overlaps meeting a P < 0.05 threshold. b, Colour indicates the significance of overlap between genes that were differentially expressed upon knockdown of an RBP and target genes with significant enrichment for 5′UTR, CDS, or 3′UTR regions in eCLIP of the same RBP in the same cell type. Shown are all 203 pairings of KD–RNA-seq and eCLIP performed in the same cell type. Hatched boxes indicate comparisons with fewer than ten genes altered in RNA-seq. The background gene set for each comparison was chosen by taking genes with at least ten reads in one of IP or input, and where at least ten reads would be expected in the comparison data set given the total number of usable reads. Significance was determined by two-sided Fisher’s exact test (or Yates’s χ2 test where appropriate) with no hypothesis testing correction (Methods). c, d, Red points indicate significance of overlap between eCLIP and KD–RNA-seq for the 13 significant overlaps (multiple hypothesis-corrected P ≤ 0.05), showing only the most significantly enriched region from b. Black points indicate knockdown RNA-seq data sets compared against enrichments for the same transcript region for eCLIP data sets for RBPs within the same binding type class (c) (as identified in Fig. 2a), or all eCLIP data sets in the same cell type (d). e, Cumulative distribution plots of gene expression fold-change for UPF1 knockdown in HepG2 (left) and FMR1 knockdown in K562 (right) for indicated categories of eCLIP enrichment. *P < 0.05, **P < 10−5; two-sided Kolmogorov–Smirnov test.
