Fig. 3

Chromatin-associated proteins bind functionally coherent sets of mRNA. RBPs differed on the degree to which they preferred to bind mRNAs versus lncRNAs. a To properly compare the two, we sampled a set of low abundance mRNAs to match the distribution of lncRNAs (referred to as mRNA_lncFPKM) and plotted the FPKM distributions for each set. b The heat map plots the Z scores of Mann–Whitney U tests comparing the distributions of fold changes for lncRNAs and low abundance mRNAs. To its right, we plot the empirical cumulative distribution functions for HUR and SUZ12. c We partitioned significantly enriched genes from all fRIP-Seqs that were also enriched by twofold or more into ten distinct groups using k-medoid clustering. A gene set enrichment analysis using DAVID found significantly enriched functional annotations for each cluster (“Materials and methods”)