To call mutations, we first modelled the background level of expression of the mutated allele by linear regression through assessment of normal B cells known to have absence of the mutation of interest.
Likewise, in the endometrium tamoxifen, but not raloxifene, may have oestogenic-like effects due to recruitment or coactivators to a subset of genes, and this aspect may vary in different tissues depending on the background level of expression of coactivators such as SRC-1 [ 21].
The instrument settings were calibrated for each run so as to obtain a background level of EGFP expression of ~1% for control cells.
The misassigned reads were spread over approximately 2500 genes on average; i.e., they contribute to a low background level of expression, although genes for nuclear proteins tended to have more such reads than other genes (Additional file 7: Table S6A).
Second, the effect of HDAC inhibitors on CD69 expression appeared to be dependent on the background level of CD69 expression, i.e., in donors with low proportions of CD69+ T-cells HDAC inhibitors induced only minimal increases, whereas CD69 expression was more inducible in donor cells with higher background proportions of CD69+ T-cells.
Background levels of expression and variability for mRNA transcripts, proteins, and metabolites in human tissues are currently not known but must be defined if toxicogenomics methods are to be used to assess personal exposures in epidemiologic studies.
In mice, the background level of SCD1 expression correlates with predisposition to liver carcinogenesis; rodents with higher levels of SCD1 are more susceptible to induction of cancer [10].
Another important direct consequence of the non-linear relationship between transcriptional activation and receptor level is that the same concentration of tamoxifen may cause significantly different effects depending on the background level of ER expression.
