Fig. 2

Intracellular depletion of MMP-2 and reduced H3NT proteolysis result in broad gene expression changes a Volcano plots generated from RNA-Seq data of U2OS pLKO.1 control versus MMP2sh1 subconfluent (− 2 days, left), confluent (0 days, middle) and over-confluent (+ 2 days, right) cells. The log adjusted fold change in expression (x-axis) was plotted relative to an adjusted p-value cutoff of 0.05 (y-axis). The number of significantly downregulated (red) and upregulated (blue) genes in the MMP2sh1 cells are indicated. b Venn diagram comparing all differentially expressed genes in the U2OS MMP2sh1 cells, relative to control, at the indicated time points. c Volcano plot of the 672 genes displaying significant expression differences throughout U2OS MMP2sh1 cell expansion relative to control. The average log adjusted fold change in expression (x-axis) was plotted relative to an average adjusted p-value (y-axis). The number of significantly downregulated (red) and upregulated (blue) genes are indicated. d Gene ontology (GO) of the downregulated (red) and upregulated (blue) genes from c. The top 10 terms (y-axis) and the number of genes in each term (parentheses) are plotted based on degree of significance (y-axis)