Table 4-2Transcriptomic BMD modeling settings and parameters that were fixed or varied in the dose concordance analysis

BMD Modeling Step / ParameterFixed/VariedValue(s)
Pre-Modeling Probe Filtering
 Maximum William’s Trend Test p-ValueaVaried0.05; 0.1
 Minimum Absolute Fold-ChangeVaried1.5; 2.0
Benchmark Dose Modeling
 Benchmark Response (BMR)Fixed1.349
 Model SelectionFixedLowest AIC (Akaike information criterion)
 Minimum Fit p-ValueFixed0.1
 Maximum BMD FilterFixedHighest Dose
 Minimum Hill Model ‘k’ Parameter FilterFixedOne Third Lowest Dose
 Maximum BMD Uncertainty FilterVariedBMD/BMDL>20; BMDU/BMDL>40
Gene Set Summarization
 Gene SetsFixedGO Biological Process
 Summary ValueFixedMedian BMD/BMDL
 Minimum Number of GenesVaried3; 5
 Minimum Gene Set CoverageVaried0%; 3%; 5%
a

The William’s trend test p-value is not adjusted for multiple comparisons.

From: 4, DEVELOPMENT OF TRANSCRIPTOMIC POINTS OF DEPARTURE FOR ETAP

Cover of Scientific Studies Supporting Development of Transcriptomic Points of Departure for EPA Transcriptomic Assessment Products (ETAPs)
Scientific Studies Supporting Development of Transcriptomic Points of Departure for EPA Transcriptomic Assessment Products (ETAPs).
Auerbach S, Casey W, Chang D, et al.
Washington (DC): U.S. Environmental Protection Agency; 2024 Mar.
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