For 'C08' secreted, transporters and secondary metabolism related categories are enriched.
The Biological process "Metabolism" was the most frequent, with other metabolic categories in the top five categories - metabolism related categories cover 68% of the terms assigned.
Other alternate exon usage changes evident at D1 are two metabolism related categories: Eicosanoid (4 transcripts) and RNA metabolism (20 transcripts, 9 are involved in RNA splicing).
Metabolism-related genes including lipid and fatty acid metabolism-related categories, as well as genes related to cellular compartments involved in nutrient absorption and metabolism, were regulated in response to the microbiota throughout the gut (figure 1E).
Enrichment of nucleotide metabolism and DNA replication related categories could also reflect the high cell division activity during the initiation of cambium in the IN3 region.
The top 200 transcripts are related to various processes including protein biosynthesis, protein metabolism, cellular biosynthesis and some stress response related categories [see Additional File 3].
With respect to our initial hypothesis that genes involved in metabolism could play a role in species divergence, we could not identify any metabolism related overrepresented functional category in the selected gene clusters.
Regards enrichment of differential expression of metabolism related genes, the largest metabolic category, was small molecule metabolism (N = 98 genes), which included the taurine transporter, SLC6A6, key enzymes in glucose metabolism (PDK4 and GLA) and mitochondrial transporters (SLC27A3, SLC25A25, SLC25A5, SLC25A6).
16 genes were cellular metabolism related genes (including five related to lipid metabolism such as apolipoprotein D and apolipoprotein R), 10 were signal transduction related genes, 45 were expressed sequence tags (ESTs) and 11 others were of various categories.
About 40%% of these differentially regulated genes in p1 and 30%% in p2 were involved in metabolism categories (CEFGHIPQ), showing almost a 10%% decrease in metabolism related genes in p2 within 1 passage, itself in a cell-free environment.
In most other metabolism-related categories, gene loss exceeded gene gain.
