BMR means “benchmark response”, which is the pre-determined response level that is considered “adverse” or “significant”. The dose that corresponds to the BMR is defined as the benchmark dose (BMD).
In an ideal case, we would know which change in response variable is physiologically significant and potentially toxic, however this is rarely known for individual genes. For 'omics dose-response analysis, the NTP recommended approach defines the BMR for a gene as the mean of the control gene expression values, plus or minus a certain number of standard deviations of the control values. The number of standard deviations is the BMR factor, and increasing this parameter increases the absolute value of the BMR for each gene. An example is shown below to illustrate the BMR, BMD and BMR factor.
In the figure above, the BMR factor is one since this is the number of standard deviations that was used to calculate the BMR.