Firstly, this generic response was not identified in the Abbott et al. [ 24] analysis because the gene expression changes for these reactions did not meet their criteria for differentially expressed genes (see Additional File 1).
This is useful because the gene expression changes that are in common, against this background of expression differences, are more likely to be relevant to the shared changes in physiology and lipid composition.
This difference in smoking status is not driving the expression of genes selected for this analysis, because the gene expression changes are observed regardless of smoking status.
Without a database to compare chemicals with unknown MOAs, the risk assessor will not be able to interpret the significance of the gene expression responses within the context of characterizing ecological risk, because many gene expression changes are not anchored to adverse effect and risk assessment requires knowledge of the MOA and dose response relationship.
Age*diet interactions appeared to be present because age-associated gene expression changes in the liver were more common in dogs fed APB (38 genes) than for dogs fed PPB (21 genes).
Because we can attribute gene expression changes downstream of BCR-ABL and TEL-PDGFRB directly to these kinases, we chose 12 genes regulated by BCR-ABL or TEL-PDGFRB for Q-PCR validation based on the fold-change in their expression, the Detection score in the gene expression as predicted by MAS 5.0, and their cellular function.
Because the clock confers on gene expression changes in activity that are not necessarily related to changes in DNA sequence, the study of circadian rhythms is inseparable from epigenetics.
We were able to evaluate inositol-mediated gene expression changes because of our simultaneous analysis of expression changes in Li-treated mice and in mice harboring KO of either IMPA1 or Slc5a3, both encoding proteins related to the PI cycle and shown to be affected by therapeutic levels of the drug.
It is a recognized problem that gene expression based classifiers do not perform well on poorly differentiated tumor samples, presumably because differentiation is driven by gene expression changes.
In mammals, these approaches may be slightly less informative than assays detecting gene expression changes, because only one out of four AGO proteins (AGO2) has the ability to cleave mRNA targets, although all AGOs mediate functional interactions 13, 95.
