To determine if the identified lincRNA-protein interactions have a functional role, we examined the effects on gene expression resulting from knockdown of individual lincRNAs that are physically associated with particular chromatin complexes and from knockdown of genes encoding the associated complex itself (see Methods). For >40% of these lincRNA-protein interactions, we identified a highly significant overlap in affected gene expression programs compared to just ~6% for random lincRNA-protein pairs (see Methods, Supplemental Table 19). Other cases may reflect the limited power to detect the overlaps, because specific lincRNA-protein complexes may be related to only a fraction of the overall expression pattern mediated by the chromatin complex.
