Fig. 3

Depletion of PDPK1 using the dTAG method reduces expression of mitotic genes (a) Volcano plot showing data for all genes detected following depletion of PDPK1 in CHP-134 cells using 500 nM dTAG47 for 24 h. Red dots are genes that significantly changed (FDR < 0.05) and dotted lines indicate the following: FDR = 0.05 and fold change = 1.5. (b) Volcano plot showing data for all genes detected following treatment of parental CHP-134 cells with 500 nM dTAG47. Dotted lines are indicated as in (a). (c) Venn diagram comparing the number of genes that overlap between RNA-seq data obtained from degrading PDPK1 in CHP-134 using dTAG47 (D47) versus addition of D47 to parental CHP-134 cells. “Up” indicates genes that were significantly increased in expression while “Down” indicates genes that were significantly decreased in expression (FDR < 0.05). (d) Gene ontology term analysis using David Bioinformatics Resource for genes that significantly decreased in expression following degradation of PDPK1. Number of genes in each category are displayed next to the bar. (e) Venn diagram comparing the number of genes that significantly decrease after degrading PDPK1 for 24 h in U2OS [12] or CHP-134 cells. (f) Gene ontology term analysis using David Bioinformatics Resource for the 95 genes in (e) that are commonly decreased between U2OS and CHP-134 cells. (g) Gene enrichment analysis for the 95 genes in (e) using ShinyGO [19], GO: Biological Process. (h) Gene enrichment analysis for the 95 genes in (e) using ShinyGO [19], GO: Cellular Component. (i) Magnitude of change in expression for the 95 genes in (e) in U2OS cells and CHP-134 cells. Data are plotted as a box-and-whisker plot and line represents the median with whiskers shown at minimum and maximum points