For example, there have been demonstrations of how 2-D gel electrophoresis analyses in RNAi studies can enable researchers to track the up- and down-regulation of proteins as a result of knockdown. Presently, antibody-based Western blot is the tool generally used to evaluate protein knockdown. Phenotypic assays, including morphological assays, enzymatic assays, biochemical assays, and cell-based assays, are also widely applied to examine the effects of RNAi knockdown.
Although most researchers are just employing quantitative real-time PCR, the fastest growing research segment involves the combination of mRNA, protein, and phenotypic assays. It is estimated that, in 2005, slightly over 60% of RNAi screens involve only mRNA analysis. However, in 2012 it is forecasted that slightly over 15% of RNAi screens are likely to involve only mRNA analysis, whereas over 70% of RNAi screens are likely to involve a combination of mRNA, protein, and phenotypic assays.