In the first discrete temporal association analysis, differentially expressed microRNAs from each time point were paired with differentially expressed targets (predicted and validated) at each time point. To maintain consistency with previous analyses, we used linear fold changes and an FDR cutoff of 0.05 for targets DE at 0 or 8h and a nominal p value cutoff of 0.05 for targets DE at 120h. (Previously, these thresholds were chosen in order to maximize the amount of information we could extract from the data. Since the 120h time point did not produce any DE mRNAs after correction for multiple comparisons, implementing an FDR cutoff for all time points would have excluded this entire time point from analysis. Thus, we chose to utilize an FDR threshold where possible and a nominal p value otherwise. Although this is a pitfall in our study, we reasoned that it would allow us to utilize all of our data while maintaining as much rigor in the analysis as possible.) Only microRNA-mRNA associations consistent with changes in microRNA proceeding changes in mRNA were considered. For example, microRNAs
