For the analyses conducted to determine whether the scoring of the staining was reproducible, we calculated separately for each marker the proportion of slides that were scored consistently by the two pathologists and estimated the Cohen's kappa statistics using expression in two categories (expressed vs. not expressed) as for the other analyses.
In accordance with Ramnath et al (2001), we analysed the MCM expression in four categories.
Treatment with MDMA also increased gene expression in GO categories related to cell signaling (e.g., neuropeptide signaling pathway and calmodulin-dependent protein kinase activity).
Distributions of gene expression in all categories containing an Enh or PrL candidate are significantly higher than those with no associated candidate.
Despite the predictable patterns of differential gene expression in aforementioned category 8 (detoxification) and 11 (actin-collagen-MMP) genes, category 1 (cancer) did not follow such pattern, due to high complexity of gene interactions in this category, with multiple cancer-promoting and –suppressing genes being simultaneously affected by dietary gluten changes.
Lipoxygenases appeared to be responsible for differential expression in the category "response to JA stimulus", which is consistent with the result in the category "fatty acid biosynthesis".
To characterize gene expression in each category, TC Annotator List (Porcine version 14.0 3-11-10) was downloaded from the TIGR gene Indices.
Overall, 26,681, 17,990, 26,162 and 26,772 predicted transcripts showed positive expression in each category respectively.
In particular, ENR caused a pronounced increase in expression of genes in categories I (lipid metabolism), J (translation, ribosomal structure and biogenesis), and L (DNA replication, recombination and repair).
Additionally, we also generated separate predictions based on co-expression in specific categories of experimental conditions, such as root cell types or nutrient environments, leaving out overall trends in correlation across all experiments.
