The intial curve fitting and BMD calculation are done at the gene level (geneBMD). However, the main statistic of interest is usually the dose at which the whole-transcriptome is responding to chemical exposure, or the transcriptomic point-of-departure (tPOD). The NTP report defines the tPOD based on pathway enrichment analysis of the geneBMDs (see Pathway BMD Analysis for more details).
However, with many ecological species these pathway-based tPODs are unstable due to the low number of annotated gene sets compared to popular mammalian model organisms, and thus it has been proposed to estimate a statistical tPOD based on the distribution of geneBMDs. There are three different methods for estimating statistical tPODs in FastBMD:
- tPOD20: the tPOD is equal to the 20th lowest geneBMD value
- tPOD10th: the tPOD is equal to the 10th percentile of the geneBMD values
- tPODmode: the tPOD is equal to the mode of the first peak in the distribution of geneBMD values
