Fig. 3

Comparison of the global gene expression profiles – a comparison of primary AML cells sampled before treatment (day 1), after treatment with ATRA alone (day 3) and after triple therapy with ATRA, valproic acid and theophyllamine (day 8). Each part of the figure shows the results for one analysis. The upper part presents the comparison of pretreatment samples and cells collected after 2 days of ATRA therapy (day 3 versus pretreatment samples), the middle figure show the effect of adding valproic acid plus theophyllamine to the ATRA therapy (day 8 versus day 3 samples) and the lower figure shows the effect of the triple combination (pretreatment samples versus AML cells sampled on day 8). The same strategies were used for all three analyses. Differentially expressed genes were first identified by SAM, and the functional analyses of the encoded proteins were based on the Panther database. Only genes encoding annotated proteins were included in these analyses. The figures thus present the representative distribution of the genes with known functions that showed differential expression according to the Panther protein class (PS) category..The name of each of the identified classes is given in the figure along with number of genes in each category. Only classes containing ≥ 2 genes are named. The genes included in each of the five major classes nucleic acid binding, transcription factor, enzyme modulator, hydrolase and receptor are listed in Table 2, and important biological functions of individual genes are described in Additional file 1: Table S6