Fig 2. Inferred RBP-mRNA interactions improve accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cell lines.

While RBP^plus models improve accuracy (R²) in predicted protein abundance over RNA^only models, improvements attained by RBPs were not distinguishable from those by randomly sampled proteins, for the majority of genes considered in the three panels. The proportion of genes where actual RBPs produced higher accuracy than random protein predictors (q < 0.05) increases from 0.65% in the NCI-60 panel to 4.2% in the normal tissue panel. (A) Distribution of R² coefficients for the actual RNA^only and RBP^plus models as well as for the RBP^plus models randomized either by permuting sample labels (RBP^plus_r.by.sample) or by randomly sampling proteins in place of actual RBPs (RBP^plus_r.by.RBP). (B) Histogram of statistical significance estimates for the RBP^plus models which were obtained randomizing the actual RBP^plus models by randomly sampling proteins. (C) Histogram of statistical significance estimates for the RBP^plus models which were obtained randomizing the actual RBP^plus models by permuting sample labels. Dashed line corresponds to the number of genes expected in each bin under the assumption of a uniform distribution.