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Figure 4 | Journal of Ovarian Research

Figure 4

From: Analysis of the levels of lysine-specific demethylase 1 (LSD1) mRNA in human ovarian tumors and the effects of chemical LSD1 inhibitors in ovarian cancer cell lines

Figure 4

Differential expression of genes involved in cell cycle and the immune/inflammatory response associated with LSD1 mRNA overexpression in the TCGA ovarian cohort. (A) Heatmap showing hierarchical gene clustering analysis of expression profiles for n = 243 genes positively and n = 215 genes negatively correlating with LSD1 mRNA expression in n = 115 low and n = 115 high LSD1-expressing ovarian tumors (source: TCGA). Genes positively correlating with LSD1 are in the top-half section of the heatmap, while genes negatively correlation with LSD1 at the bottom-half section after clustering. Genes in this analysis were included based on: 1) showing differential expression (fold-change) >1.5 for overexpressed or <1/1.5 for underexpressed genes between the two sets of high and low LSD1-expressing tumors; 2) reaching a Delta = 3 in the comparison between both tumors sets by SAM analysis, which corresponds to FDR = 3e-05; and, 3) correlating with LSD1 expression in at least 50% tumors (both directions). The values of expression for each gene were independently normalized between the maximum (+1, or bright red) and the minimum expression levels detected (−1, or bright green) for the same particular gene (see legend), which does not allow absolute (but only relative) quantitative comparisons among genes. Therefore, overexpression is shown in red and underexpression in green. (B) List of most-enriched gene ontology (GO) terms in the set of n = 243 genes positively (top panel, red) and n = 215 genes negatively or inversely (bottom panel, green) correlating with the pattern of LSD1 mRNA expression. GO terms shown in the left. The x-axis refers to p-value of enrichment.

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