Fig. 2: Transcriptomic (RNA-sequencing) and quantitative mass spectrometry (MS)-based proteomic analysis of HSP90α/β-KO cells. | Cell Death & Disease

Fig. 2: Transcriptomic (RNA-sequencing) and quantitative mass spectrometry (MS)-based proteomic analysis of HSP90α/β-KO cells.

From: Co-targeting HSP90 alpha and CDK7 overcomes resistance against HSP90 inhibitors in BCR-ABL1+ leukemia cells

Fig. 2

A Volcano plot showing significantly (FDR <0.05; log2(FC) < −1 or log2(FC) > 1, calculated using edgeR (F-Test & Benjamini-Hochberg correction) up- or down-regulated genes from RNA-sequencing data (obtained from three independent replicates) of HSP90α-KO compared to empty vector (EV) control K562 cells. Black dots represent genes that are not significantly regulated, while gray dots represent significantly regulated genes, but below log2(FC) threshold. Blue and red dots represent significantly downregulated and upregulated genes, respectively. B fGSEA on the RNA-seq data of HSP90β-KO cells, displaying significantly (FDR = 0.05) regulated ontology gene set signatures in comparison to EV control. C Volcano plot obtained from five independent replicates of HSP90α-KO compared to EV control K562 cells showing up- or down-regulated proteins based on MS-based proteomics data applying p-value < 0.05 and log2(FC) < −1 or log2(FC) > 1 as the specificity cutoff criteria. D Gene clusters obtained using clusterProfiler on the MS data of HSP90α-KO cells revealed significant downregulation (FDR = 0.05) of energy metabolism signature. Normalized enrichment scores (NES). Tables showing consistently up- or down-regulated genes in HSP90α-KO (E) or in HSP90β-KO (F) K562 cells from the RNA-seq and MS-based proteomics analysis.

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