Figure 2. Comparison of transcription profiles of ATRA-induced granulocytic differentiation in HOTAIRM1 knockdown and control NB4 cells. (A) Principal component analysis (left) and scatter plots of log ratios (right) of ATRA-induced gene expression changes in knockdown and control cells (red, significantly upregulated genes; blue, significant downregulated). In the scatter plots, b indicates slope (i.e., dissimilarity) and r² represents the square of the correlation coefficient(fitness); (B) Hierarchical clustering of genes for which expression in ATRA-induced NB4 cells was significantly altered by HOTAIRM1 knockdown, as evaluated by moderated t tests between knockdown and scramble control. Each column of the heat map presents data from an independent control or knockdown clone. The bars on the left margin indicates genes for which HOTAIRM1 knockdown abated ATRA-induced downregulation (orange) and upregulation (blue). Individual genes of interest are noted to the right of the heat map; colored bars in the right margin mark the positions of genes in the indicated DAVID functional annotation clusters representing the indicated (top margin) enriched functional terms. The graphs to the right of the heatmap show the top DAVID functional annotation terms for genes for which HOTAIRM1 knockdown abated ATRA-induced downregulation (top, orange) and upregulation (lower, blue), with the significance of the enrichment indicated by the position on the x-axis (-log EASE), the fold enrichment indicated by the intensity of color, and the number of genes indicated by the size of each dot; (C) Time course of MS4A3, CDC7, HOXD13, and BCL6 gene expression during maturation in NB4 cells at the indicated days of ATRA induction in HOTAIRM1 knockdown and control cells, as indicated by symbols and colors in the insert (mean ± SD, n = 3–9; * P < 0.05, two-way ANOVA Holm–Sidak post-hoc test). ctl, non-transduced control; scr: scramble control; kd, HOTAIRM1-knockdown cells; dCTL/dSCR/dKD, differentiated ctl/scr/kd (4 d in ATRA).