Fig 1: Experimental Validation of Regulatory Interactions among Protein Complex SubunitsRate-limiting interactions within the adaptor protein complex 3 (AP3) and the transcription initiation factor IIE (TFIIE) complexes.(A and C) Correlation of the copy-number profile of the regulatory protein with the protein residuals of the regulated protein (left plot) and agreement at the protein level between the two proteins (right plot).(B and D) shRNA knockdown of the regulatory proteins, AP3B1 and GTF2E2, show strong decrease in the protein abundance of the regulated proteins, AP3M1 and GTF2E1, respectively. Knocking down GTF2E1 showed a significant downregulation of GTF2E2, indicating a bidirectional relation between those proteins. In contrast, AP3M1 shRNA did not affect AP3B1 protein abundance. Protein abundance changes are measured and quantified by western blot using antibodies specific for the corresponding proteins. The quantified bands in the shAP3B1, shAP3M1, shGTF2E2, and shGTF2E1 experiments were scored relative to the control shRNA (shNT). GAPDH was used as a loading control.Error bars shown are the SD from the mean (n = 3 independent experiments). ∗p < 0.05 compared with shNT, two-tailed unpaired t test.