The resulting L1000 signature was used to calculate the targeted landmark gene down-regulation and rank relative to all other shRNAs in the experiment. For each gene in each sample, we computed differential expression values (z-scores) by comparing the gene's expression value in the given sample to that same gene's expression values in all other samples in the cohort and then collapsed replicate samples (DSLM-KD). The resulting dataset contains, as columns, an individual shRNA targeting a landmark gene performed in either MCF7 or the PC3 cancer cell line. Rows are replicate-collapsed z-scores (level 5, see below) of all measured landmark genes.
