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. Author manuscript; available in PMC: 2023 May 18.
Published in final edited form as: Toxicol Sci. 2021 Apr 27;181(1):68–89. doi: 10.1093/toxsci/kfab009

Figure 3. Reproducibility of high-throughput transcriptomics data.

Figure 3.

(A-B) Pairwise correlations of log2 CPM values by treatment group. All correlations were calculated between individual samples of the same treatment group as indicated. The BLTSA:BLDMSO group shows the correlation between samples from different treatment conditions. (C-D) Density distribution of the D-statistic by treatment group. (E) Correlation of L2FC (orange bars) and ssGSEA signature scores (blue bars) in each of the three test plates to median L2FC and ssGSEA signature scores across all test plates. L2FC values and ssGSEA scores for each treatment group were calculated relative to the bulk lysate DMSO (for bulk lysate TSA treatments) or DMSO (for Genistein, Sirolimus, or Trichostatin A treatments) controls as described in the methods. BLDMSO = bulk lysate DMSO control; BLTSA = bulk lysate Trichostatin A; DMSO = DMSO control; GEN = Genistein; SIRO = Sirolimus; TSA = Trichostatin A.