Specifically, for each gene we computed a t-statistic between shRNAs targeting the lincRNA and control shRNA samples. To assess the significance of each gene we permuted the sample and control groups retaining the relative sizes of the groups and computing the same t-statistic. We then assigned an FDR value to each gene by computing the average number of values in the permuted t-statistics that were greater than the observed value of interest and divided this by the number of all observed t-statistics that were greater than the observed value. We defined genes as significantly differentially expressed if the FDR was <5% and the fold-change compared to the negative controls was >2-fold. Using this approach, an effect would only reach a significant FDR if the scale is significantly larger than would be observed in the negative controls. Knockdown of a lincRNA was considered to have a significant effect of gene expression if we identified at least 10 genes that had an effect that passed all of the criteria.
