To determine relationships between lincRNA knockdowns and functional states, we employ a modified Gene Set Enrichment Analysis34 approach that accounts for the continuous nature of the two datasets, similar to previously described extensions34,64,65. For each lincRNA knockdown by functional pair we compute a continuous enrichment score. Specifically, (i) for each lincRNA knockdown we compute a normalized score matrix compared to a panel of negative control hairpins by computing a t-statistic for each gene between the replicate lincRNA knockdown expression values and the control knockdown values. (ii) For each experiment, we sort the matrix by the normalized score such that the most differentially expressed upregulated gene is first and the most differentially expressed downregulated genes is last. Using this ordering we sort the functional dataset such that the ordering corresponds to the differential rank of the lincRNA knockdown set. (iii) We compute a score Si as the running average of values from the first position to position i. We then define the enrichment score E as the maximum of the absolute value of Si for all values of i>10. We require
