% All genes % Active in both % Exclusively pre-pro-B % Exclusively pro-B % Inactive in Both   Transcriptional (1) 4.0 2.8 52.0 22.4 5.3 All Genes Post-transcriptional (2) 6.1 5.5 8.4 6.0 10.7 Undetermined or ambiguous mechanism (3) 1.5 1.2 0.0 1.9 6.9 No protein change (4) 88.4 90.6 40.0 68.2 73.0 Transcriptional (1) 34.6 29.9 86.7 70.6 19.6 DE (iTRAQ) genes Post-transcriptional (2) 52.5 58.0 13.3 23.5 54.9 Undetermined or ambiguous mechanism (3) 12.9 12.1 0.0 5.9 25.5

Table 1: Mechanisms of differential protein abundance. The percent of all genes (top) and of genes with protein differential abundance (‘DE’, bottom) that fall in the broad regulatory groups: ‘transcriptional’, ‘post-transcriptional’, ‘undetermined or ambiguous mechanism’, and ‘no protein change’, as determined in Supplemental Table 1.