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To obtain an overview of the main biological processes affected by HDACi, the gene ontology terms (GOs) overrepresented amongst up- and down-regulated consensus genes (p < 0.05) were grouped into 7 superordinate cell biological processes (e.g. neuro nal development), mesoderm al development)) and the number of GOs in each category was counted.

Interestingly, only the "unknown molecular functions" term was significantly under-represented amongst up-regulated genes (Table 1).

For Alethea treatment, "response to biotic stimulus" , "defense response" and "response to stress" were over-represented amongst up-regulated genes.

Panel (E) shows an enrichment (p  < 0.0001) of particular transcription factor binding sites amongst up-regulated genes.

Panel (B) shows an enrichment (p  < 0.0001) of IRF7 transcription factor binding sites amongst up-regulated genes.

Panel (F) shows an enrichment (p  < 0.0001) of NF-kB transcription factor binding sites amongst up-regulated genes.

When HDACi consensus genes were examined, neuronal TF were most highly represented amongst down-regulated consensus genes, while ESC TF was most highly represented amongst up-regulated genes (Suppl. Fig. S9B, C).

Concerning GO terms enriched amongst up-regulated probes, it is worth to mention the over-representation of genes involved in biological processes such as immune response, cell response to stimuli, apoptosis and cell death, cell motion/migration/adhesion, and regulation of cell differentiation (Additional file 10).

Notably, many TFBS were overrepresented amongst the up- and down-regulated genes (e.g. SOX9, FOXD3) (Suppl. Fig. S4).

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