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The sRNA pathways have higher activity in female than in male cones, and the miRNA pathways are the main sRNA pathways in P. tabuliformis.
The expression profiles of these genes suggested that the sRNA pathways have higher activities in female than in male reproductive structures.
Edge weights w e) depend on our confidence that a specific interaction exists (Supplementary Table S1) so that more confident pathways have higher weights (Gitter et al., 2011).
In this study, we find that genes involved in osteoblast development, hair follicles development, pigmentation, spermatid, nervous system and organ development, and some metabolic pathways have higher levels of population differentiation.
Proportionally, the male cones had relatively high levels of 24-nt sRNAs (Fig. 5), but AGO4, which plays a key role in the action of 24-nt sRNAs, was expressed at a very low level in male cones (Fig. 4a), indicating that both miRNA and siRNA pathways have higher activities in female than male cones.
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It indicates that these four pathways have high percentages of DE genes.
For mmu04060, the analysis of lung adenocarcinoma tissue specimens have demonstrated that the genes involved in these biological pathways have high rates of over-expression [ 57].
Whereas some oncogenic pathways have high correlations to breast cancer subtype (RAS, CTNNB1, p53, HER1), others have high variability of activity within a specific subtype (MYC, E2F3, SRC), reflecting biology independent of common clinical factors.
When the best precision achieved by any of the multiple-species nodes was compared to the best of the single organism nodes for each pathway, the majority of pathways had higher precision for a multiple-species node.
The actual genomic arrangement of the biological pathways had higher C values (vertical dashed lines) than the vast majority of those with different extents of reshuffling (colored solid lines), for both the overall and remote gene pairs.
For example GeneGo pathways display a higher value for M on interactions drawn from CellMap and STRING (M = 1.65, 1.91) than on GeneGo interactions (M = 1.47); Reactome pathways had higher Modularity on STRING, GeneGo, and I2D interactions (M = 1.71 to 4.85), than on Reactome (M = 1.15).
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