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. Author manuscript; available in PMC: 2015 Nov 20.
Published in final edited form as: Cell. 2014 Nov 6;159(5):1126–1139. doi: 10.1016/j.cell.2014.10.024

Figure 3. THZ1 Causes Massive Downregulation of Actively Transcribed Genes in MYCN-overexpressing NB Cells.

Figure 3

(A) Heat map of gene expression values in MYCN-amplified and nonamplified cells treated with THZ1 (100 nM for 6 hr) vs. DMSO. Rows show z-scores calculated for each cell type.

(B) Quartile box plots of log2 fold changes in gene expression in MYCN-amplified and nonamplified cells treated with DMSO or THZ1 at the same dose and duration as in (A). Box plot whiskers extend to 1.5 times the interquartile range (n=18,665 expressed genes, p<10−15 for Kelly vs. SH-SY5Y and IMR-32 vs. SH-SY5Y, two-sided Mann-Whitney U test).

(C) Venn diagram depicting the overlap between sets of differentially expressed transcripts (THZ1 vs. DMSO) in MYCN-amplified (Kelly, IMR-32) and nonamplified (SH-SY5Y) cells treated with THZ1 as in (A). Red represents upregulated and blue, downregulated transcripts.

(D) Heat map of gene expression values of transcriptional and cell cycle CDKs in MYCN-amplified and nonamplified cells treated with THZ1 as in (A) vs. DMSO. Rows show z-scores calculated for each cell type.

(E) Correlation between log2 fold changes in gene expression following THZ1 (100 nM) vs. DMSO treatment and actinomycin D (1 μM) vs. DMSO treatment for 6 hr. in MYCN-amplified NB cells. R2 (coefficient of determination) calculated using a simple linear regression model.

See also Figure S3.