Extended Data Fig. 4: Transcriptomic response to ScURA expression.
a, Principal component analysis of gene expression data from 143B cells treated with ethanol vehicle or antimycin/myxothiazol (anti/myxo). b, Volcano plots showing differentially expressed genes from ScURA vs. WT 143B cells, antimycin/myxothiazol vs. vehicle in WT cells, and antimycin/myxothiazol vs. vehicle in ScURA-expressing cells; n = 4 independent biological replicates. c, Dot plot showing the top 10 significantly enriched GO biological process terms from a GSEA of ScURA vs. WT cells. Significance was determined using a permutation-based weighted Kolmogorov-Smirnov test (one-sided). P-values were adjusted using the Benjamini-Hochberg method. d, Bar plot of the top 5 most significant upregulated and downregulated transcription factors. The activity of each transcription factor was inferred using decoupleR based on gene expression data from ScURA vs. WT cells. Scores represent the t-statistic from the uniariate linear model (Wald t-test, two-sided). e, Volcano plot showing differentially expressed genes from 143B ScURA vs. WT cells. Dots corresponding to genes whose transcription is activated by HIF1α are highlighted in red (log2FC > 0) or blue (log2FC < 0). Statistical analysis was performed using the DESeq2 R package. For panels b and e significance was determined using the Wald test (two-sided). P-values were adjusted for multiple comparisons using the Benjamini-Hochberg procedure to calculate adjusted p-values.
