Stem/progenitor cell gene expression profile synergistically preserved by VPA + Li. (A) Venn diagram representation of significantly differentially expressed genes on Li, VPA, or VPA + Li treatment. Venn diagram were created with Venny.49 (B) Rank-based heat maps of expression levels of genes up-regulated or down-regulated by VPA + Li in 4 freshly isolated cell types, stem (LSK), progenitor (L−S−K+), myeloid (Gr1+), and erythroid (Ter119+) cells. Heat maps were created with Genesis Version 1.7.6 software.50 (C) Graphic representation of gene networks affected by VPA + Li. For similarity measure, Pearson correlation was used with a threshold of > 0.85 (FDR P < .1).30 The network consists of nodes (genes) and edges (biologic relations between nodes). Size of nodes correspond to amount of connection of a particular node with other nodes. Nodes are color-coded according to their expression abundance in 4 distinct cells types, green nodes refer to genes that are preferentially expressed in stem cells (LSK), yellow nodes shows genes active in progenitors (L−S−K+), blue nodes are prevalent in mature myeloid cells (Gr1+), and purple nodes are expressed in mature erythroid cells (Ter119+). Lines represent correlations of particular genes with others, blue lines represents negative correlations, and red lines indicate positive correlations. Nodes with < 1 connection were removed. (D) TF networks significantly changed by VPA + Li treatment. This graph shows essentially the same data as those in panel C, but now only for transcriptional regulators. All network visual representation were performed with Gephi Version 0.8 beta software.31 (E) Acetylation status of histone H4 at promoter regions of HoxA7 and HoxB4 genes. β-actin was used as a housekeeping gene control for ChIP experiments.
