To determine whether independent hairpins targeting the same lincRNA gene share common gene targets, we computed a continuous enrichment score described above. Briefly, we computed a t-statistic for both hairpins against the negative controls. We then took the second best hairpin and sorted the genes. We scored the best hairpin affected genes based on this ranked order. We assessed the significance of this enrichment by permuting the samples and controls and assigned an FDR of the overlap of the expression effect (as described above).
