Journal: Toxicological Sciences

Article Title: In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals

doi: 10.1093/toxsci/kfac127

Figure Lengend Snippet: Comparison of estrogen receptor alpha (ERα) bioactivity and transcriptomic points of departure (tPODs) derived from the whole transcriptome analysis in MCF-7 cells ( n = 3–4 per concentration) exposed to bisphenol A and 15 alternative chemicals at a range of concentrations (0.0005–100 µM) for 48 h. ERα prediction is based on at least one concentration yielding an agonist or antagonist call. For tPOD derivation, data were prefiltered using the Williams trend test ( p ≤ .05) and a fold-change of ≥1.5 or ≤1.5. Data were also postfiltered with the following settings in BMDExpress v2.3: Best BMD/BMDL <20, Best BMDU/BMD <20, Best BMDU/BMDL <40, and Best fitPvalue >.1. tPODs representing the 25th rank ordered gene benchmark concentration (BMC) (shown in µM), the median gene BMC for the lowest pathway (at least 3 genes and 5% of pathway) as well as the median gene BMC for the ERα biomarker gene set are shown in the table and in the top panel. The chemicals are shown in decreasing order of potency based on tPODS from the 25th gene BMC.

Article Snippet: Data were processed as described below and reads were aligned to the BioSpyder TempO-Seq Human Whole Transcriptome probe set (22 537 probes over 19 687 genes) using their purpose-built pipeline.

Techniques: Comparison, Derivative Assay, Concentration Assay, Biomarker Discovery

Journal: Toxicological Sciences

Article Title: In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals

doi: 10.1093/toxsci/kfac127

Figure Lengend Snippet: Comparison of ERα bioactivity and tPODs derived from the whole transcriptome analysis in MCF-7 cells ( n = 3–4 per concentration) exposed to BPA and 15 alternative chemicals at a range of concentrations (0.0005–100 μM) for 48 h. ERα prediction is based on at least one concentration yielding an agonist or antagonist call. For tPOD derivation, data were prefiltered using the Williams trend test ( p ≤ .05) and a fold-change of ≥1.5 or ≤1.5. Data were also post-filtered with the following settings in BMDExpress v2.3: Best BMD/BMDL <20, Best BMDU/BMD <20, Best BMDU/BMDL <40, and Best fitPvalue >.1. tPODs representing the 25th rank ordered gene BMC (shown in μM), the median gene BMC for the lowest pathway (at least 3 genes and 5% of pathway) as well as the median gene BMC for the ERα biomarker gene set are shown in the table and in the top panel. The chemicals are shown in decreasing order of potency based on tPODS from the 25th gene BMC. 25th gene, ERα biomarker, lowest median pathway.

Article Snippet: Data were processed as described below and reads were aligned to the BioSpyder TempO-Seq Human Whole Transcriptome probe set (22 537 probes over 19 687 genes) using their purpose-built pipeline.

Techniques: Comparison, Derivative Assay, Concentration Assay, Biomarker Discovery