Number of genes (and entities) regulated by ATRA in differentiating control and TG2 knockdown NB4. (A-B) Number of annotated genes (and all entities in parentheses) regulated by ATRA in control NB4 (A) and in TG2-KD NB4 cells (B) are visualized as a Venn diagram. Two-fold change difference was set, and significantly changed genes were selected (P ≤ .05 and Bonferoni Multiple Correction was used). The numbers of up- and down-regulated genes are separated. Genes significantly regulated at the both stages of the differentiation (day 2 and day 3) are presented in the overlapping region of Venn diagram (in bold). Note that among the genes up-regulated in both stages of the differentiation in TG2-KD NB4 cells, almost 100 (307-209) genes were not up-regulated, whereas approximately 250 (1059-808) genes were not down-regulated compared with the control cells. (C) Real-time Q-PCR verification of microarray data. Fold change induction of 10 selected genes upon ATRA-treatment in control (black bars) and TG2-KD cells (white bars) are shown among the X-axis on the third day of differentiation. Left panel shows the results obtained from the microarray analysis, and right panel demonstrates a representative expression pattern of the same genes determined by real-time Q-PCR. The genes analyzed were the cell surface antigen CD36, the RARα, the TGFβ, the intercellular adhesion molecule 3 (ICAM3), the cell surface antigen CD11c/integrin αX (CD11c/ITGAX), the thrombospondin-1 (THBS1), the MER receptor tyrosine kinase (MERTK), the CC chemokines CCL3 and CCL22, and the TG2. Ratios of fold change differences of analyzed genes in the TG2-KD NB4 cells and the control cells are presented.