PMC

Prediction Agreement as a Measure of Confidence. When constructing an ROCs on protein measurements, there is an almost linear relationship of the resulting AUCs and prediction agreement. This is also true for mRNA measurements, though the slope is less steep.

Correlation of Predicted miRNA Targets with Hosts. The PI3K - PKB/AKT pathway is believed to be a key component in cancer development. We compared correlation of miRNA predicted targets (prediction agreement ≥ 2) to the respective host in normal (N) and tumor (T) tissue. Several of the hypothesized targets display features predicted by our model, such as AR, PDGFB, PDGFRB, AKT3 and MAPK1.

Intragenic miRNA Properties. (a) The sizes of host gene introns closest to the TSS are significantly larger than those of respective controls. (b) Intronic miRNAs appear to be unevenly distributed across the intronic regions of their host genes. More then half of intronic miRNAs are located within the first five 5' introns of their hosts. (c) The observed target coverage (diamond) is at the upper end of the random distribution of target coverages for different signaling pathways, indicating that intragenic miRNAs have more targets within the pathway than would be expected by chance. (d) Intragenic miRNAs may control their host in the setting of a negative feedback circuitry not only through direct regulation of the host's transcription, but also on the order of the interactome, by controlling other genes in the host's pathway.