They also broke down a collection of molecules called metabolites, which form as a product of metabolism and can hint at where metabolic processes go wrong.
Moreover, GO terms for RNA processing (GO: 0006396), ncRNA processing (GO: 0034470), rRNA metabolic processes (GO: 0016072), rRNA processing (GO: 0006364), and maturation of SSU-rRNA (GO: 0030490) were over-represented with high levels of transcripts.
The most enriched terms of biological process ontology were metabolic processes, such as carbohydrate metabolic processes (GO: 0005975), DNA metabolic processes (GO 0006259), cellular macromolecule metabolic processes (GO 0044260), and nucleic acid metabolic processes (GO 0090304).
We find that for the 98 genes detected on both mRNA and protein levels in the two datasets, there is a significant enrichment for genes involved in metabolic processes (GO ontology reference) when compared to genes expressed on the mRNA level alone (Table S1).
Most of the biological process categories were related to metabolic processes (GO: 0008152, 23.23%) and cellular processes (GO: 0009987, 23.68%).
Indeed, there are 10,140 sequences associated with metabolic processes (GO level 2) and 8,376 sequences related to cellular processes.
For the induced gene set, the most prevalent GO categories were oxidation-reduction (GO: 0055114), trehalose metabolic processes (GO: 0005991), and lipid transport (4 genes, GO: 0006869).
In the Biological Process category, the majority of transcripts were involved in cellular protein metabolic processes (GO: 0006464) and signal transduction processes (GO: 0007165).
Enrichment for the TGFβ pathway was linked with Cluster 5 as well as regulation of phosphate metabolic processes (GO BP), Golgi (GO CC) and regulation of transcription (GO MF).
GO analysis of the strongly upregulated genes in clusters 2 and 3 resulted in the identification of ncRNA metabolic processes GOs (see Table 1).
