Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations.
This is due to the fact that gene expression patterns are highly tissue-specific and gene expression measures in blood may not totally reflect the regulatory machinery in brain or other related tissues.
Because the measures of gene expression themselves cannot be directly compared among different platforms [ 51], we found that the use of rank comparison tests can serve as a way to increase the number of regulated genes given that similarities in gene regulation are made less dependent on the magnitude of change or the gene expression measures themselves.
(a) Reporter gene expression measured in luminescence/colony-forming units (CFU), relative to the minimum expression (mean±s.e.m., n=5).
PBMCs were isolated, RNA extracted and gene expression measured using RNAseq.
Because gene expression levels were measured in total adipose tissue, we confirmed the cell specificity of the M2-markers with immunostaining in a random selection of the available postmortem biopsies.
Nevertheless, when measuring steady-state levels of mRNA, one should keep in mind not to overestimate chemical toxicity on other organization levels (cells, individuals and population), because gene expression alone can sometimes be a poor predictor of protein abundance [34].
Because serial analysis of gene expression (SAGE) measures absolute levels of transcripts, cross-comparison of SAGE data is possible across experiments and laboratories [ 26].
Caution should be used when interpreting this data because the protein-coding gene expression was measured by tiling arrays and the piRNA cluster expression by RNA-seq.
Because the gene expression data were measured in multiple samples, with the addition of some actin genes represented by more than one corresponding probes, the average value of actin gene expression using every probe in all samples was adopted as the expression level for this actin copy in each tissue.
