iLINCS analysis.

To compare the transcriptomic changes caused by our drugs to other perturbations, we used the Library of Integrated Network-based Cellular Signatures (iLINCS) (25) data portal to identify genes dysregulated by HDAC treatments. We identified 180 genes that were consistently up- or down-regulated as a result of treatment with 8 different HDAC treatments (trichostatin A, vorinostat, panobinostat, dacinostat, romidepsin, belinostat, entinostat, mocetinostat) across analyzed cell lines, and determined the gene expression shifts of these genes as a result of HDAC and BET inhibitor treatment in our cell lines. We additionally used the connected perturbations analysis function of iLINCS to identify compounds eliciting gene signatures similar to those in our study using lists of significantly differentially expressed genes (Adj. P < 0.05, log₂ FC > |1.5|).