In total, 11 of the 13 genes have higher chromatin accessibilities in the Tet1 group, whereas only 2 of the 7 genes have higher chromatin accessibilities in the Tet1 group (Fig. 4i).
In contrast to the predictive markers replicated above, most of these 141 genes have higher expression in most subjects with bacterial infection.
We screened the functional categories and metabolic pathways where Sc- or Sb-type genes have higher expression levels than the corresponding orthologous genes.
Thus, it appears that cytokinesis genes have higher prognostic value than other mitotic genes and genes required for chromosome integrity.
Expression breadth, however, shows a contrasting pattern, i.e. longer genes have higher breadth of expression, possibly to ensure those structural features associated with gene plasticity.
While two gibberellin-related genes have higher transcript levels in 35S::PCN-miRNAd, one (GA 20-oxidase, fgenesh4_pm.C_LG_II000702) is putatively involved in GA biosynthesis [42] while the other (GA 2-oxidase, estExt_fgenesh4_pg.C_LG_XI0670) is putatively involved in GA catabolism [43].
To test the gene model illustrated in Supplementary Figure S3, we asked how many genes have higher tag density in the gene body compared to its upstream and downstream regions.
We showed that many inflammation-related genes have higher levels of expression until 3 days post-trauma while genes related to osteoblast and osteoclast activity increase at day 4 and thereafter.
Our results confirmed this observation, highlighting that essential genes have higher degree and closeness and lower eccentricity compared to complex disease genes (P = 2.6×10−8; 1.5×10−9 and 7.1×10−4 respectively).
We find that these 117 putatively diet-related genes have higher absolute effect sizes (mean differences between groups in units of standard deviation) for human-chimpanzee expression differences than 1,052 non-diet-related genes differentially expressed between human and chimpanzee livers (one-sided Mann-Whitney U test p = 0.022).
Consequently, modification and remodeling cohort genes have higher gene activity.
