Fig. 4.

Proteome remodeling upon tunicamycin treatment involves hundreds of significant expression changes. (A) Volcano plot comparing protein expression levels in samples treated with vehicle to those with the highest tunicamycin concentration (5 μg/ml). Proteins significantly upregulated upon tunicamycin treatment are shown as red dots, those downregulated as green dots. The curve is derived at FDR=0.05 and s₀=0.5 as described in the Materials and Methods section. Under these conditions, the UPR protein calnexin is significantly upregulated as expected (CANX, blue square, see text). The dataset was filtered for 50% valid values in at least one group. eIF4G1 is marked with a black square, MAFF and CHOP were excluded by the filtering procedure (see Fig. 3E). (B) Unsupervised hierarchical clustering of 238 proteins with significantly different levels of expression between DMSO- and tunicamycin (5 μg/ml)-treated HeLa cells (median of N=3 biological replicates). Profiles of the proteins in the clusters and corresponding relative enrichments are indicated to the right. Enrichment is based on Fisher's exact test of keyword annotations at FDR=0.04.