To determine the functional overlap between the lincRNA and the chromatin complexes it physically interacts with, we compared the effects on gene expression upon knockdown of the lincRNA and the associated protein complex. To do this, we utilized the gene expression profiles determined for each lincRNA knockdown and knockdowns of 9 of the 12 identified chromatin complexes for which we had good hairpins. We defined each interaction between a lincRNA and protein, and compute a continuous enrichment score, generated all permutations of the control hairpins and sample hairpins and assigned a false discovery rate to the scores (as described above). At an FDR<0.05 we identified 43% of the interactions to be significant. For 69% of the interactions, we were able to identify an overlap at an FDR<0.1.
