Changes in gene expression at the onset of MEDEP differentiation. (A) MEDEP differentiation induction by growth factors. MEDEP cells were treated for 72 hours with SCF and dex or Epo or, where indicated, for 12 hours only with Epo in the presence or absence of succinyl acetone (SA) and then with SCF+dex after removal of Epo. After 72 hours, hemoglobinization was monitored by benzidine staining and cell viability by trypan blue exclusion. (B) Two-dimensional annotation enrichment analysis of the proteome modifications occurring during the first 12 hours in MEDEP and primary cell differentiation was performed, using the Uniprot Keywords database (supplemental Table 1). This method identifies annotation terms whose corresponding proteins exhibit consistent behavior in 1 data set and analyzes the behavior of all proteins with the same annotation in a second data set, thus enabling the detection of similarities or divergences. (C) Venn diagram showing the mRNA and proteins with a significant modification during the first 12 hours of MEDEP differentiation. Only gene expression quantified at both the transcriptomic and the proteomic level were used for this analysis. (D) Two-dimensional annotation analysis of the transcriptome and proteome modifications during the first 12 hours of MEDEP differentiation. (B,D) Keyword annotations corresponding to the numbers on the main graph (right). (E) Hierarchical clustering analysis of the proteins differentially expressed after 12-hour incubation with Epo (T12H) or with Epo and SA (T12HSA), compared with cells incubated with SCF and dex (T0) (z-score–transformed values).