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Figure 3 | Genome Biology

Figure 3

From: Differential protein occupancy profiling of the mRNA transcriptome

Figure 3

Global comparison of protein occupancy profiles and mRNA expression levels in MCF7 and HEK293 cell lines. (A) Heatmap of average pairwise Spearman correlation coefficients of protein occupancy profiles computed for biological MCF7 and HEK293 replicate experiments. The correlation was computed using a sliding window approach to compare read coverage of transcripts between two experiments. The median correlation over all transcripts is shown. (B) Fraction of reads mapping to 5' UTRs, coding sequence (CDS) and 3' UTRs in MCF7 (left) and HEK293 (right) cells averaged over all replicates. Read distributions for protein occupancy profiling experiments are shown on top, while reads from mRNA-seq experiments are depicted at the bottom. (C) Density distribution of T-C transitions from protein occupancy profiling experiments (top) and mRNA-seq read coverage (bottom) averaged over all covered transcript regions. Bold lines represent densities from MCF7 cells. Dashed lines represent densities from HEK293 cells. (D) Smooth scatterplot of gene-wise read abundance changes between MCF7 and HEK293 from protein occupancy profiling (y-axis) and mRNA-seq (x-axis) data. The red line represents the best linear fit. The Pearson correlation coefficient is indicated. It is apparent that RNA-seq data cannot account for the variability in the protein occupancy profiling data.

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