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We discuss the biological relevance of the most enriched groups below.
The most enriched groups from Table 2 are translation, glycolysis, RNA processing, actin filament-based processes and mRNA metabolic processes (P-values of 2.8 × 10-28, 5.1 × 10-12, 1.1 × 10-9, 2.5 × 10-8 and 3.6 × 10-7, and fold-enrichment of 10.2, 21.6, 4.2, 6.0, and 4.3, respectively; see Table 2).
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In the bacteria, the Proteobacteria was the most enriched group [ 45, 46] followed by Firmicutes and Bacteroidetes/Chlorobi group in that order.
Apart from these unclassified genes, C-compound/carbohydrate metabolism and transport genes were the most enriched group (P-value <1E-9), as expected.
Raj et al. found that proteins, such as glutathione- S-transferase-P1 and carbonyl reductase 1 that are involved in the cellular response to oxidative stress were the most enriched group after PL treatment, suggesting a mechanism based on reactive oxygen species (ROS).
The second-most enriched group corresponds to the HSP70 family (36 predictions out of 107, p-value of 1.7 x 10−13).
The third-most enriched group includes the stress-induced Srp1p/Tip1p family (16 predictions out of 40, p-value of 2.0 x 10−6).
The fourth-most enriched group (36 predictions out of 185, p-value of 3.9 x 10−6) represents a subset of the major facilitator superfamily, more specifically genes that code for H+ antiporters.
Genes related to the cellular structure are among the most enriched functional groups, such as nuclear envelope and cytoskeleton.
The most enriched functional groups of genes amongst the miRNA targets, and the canonical pathways within which they play a role, are provided in Figure 1.
Similar to our previous study using microarray-based analyses, genes for homeobox proteins and the WNT signaling pathway were among the most enriched functional groups [10].
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