The ranking of genes was performed with T test, with an absolute mode for gene list sorting.
Together these results show that gene repression is a common mode for gene regulation among the genes that have the most significant survival effect in GBM.
Instead, our results demonstrate that gene repression, rather than activation, is a common mode for gene regulation among the genes that have the most significant effect on survival in GBM.
We have previously shown, through this type of cluster analysis, that binding sites can be classified based on a series of factor recruitments, enabling the highlighting of commonalities in regulatory modes for modulated genes in each specific cluster [ 28].
This study found evidence for all modes of gene action, including dominant and transgressive (especially overdominant) allelic interactions contributing to parental expression divergence.
Previous studies for comparing different modes of gene duplication often assigned a unique origin to each duplicate gene (Guan et al. 2007; Hakes et al. 2007; Wang Y, et al. 2011).
Given that H3K27ac was most variable between the chromatin-based gene clusters and also most dynamic upon EWS-FLI1 knockdown, we hypothesized that the clustered genes should respond differently to induced global changes of acetylation, which would support the clusters' usefulness for identifying distinct modes of gene regulation among EWS-FLI1 target genes.
One limitation to the comparison is that all high-throughput genetic screens for modifiers were performed in different model organisms and used very different screen set-ups, including different modes of gene targeting and scoring for different phenotypes (Table 2).
Two modes of gene organization have been observed for the discontinuous rRNA genes.
With the "five sites mutation" mode for opsin gene evolution, the probability of speciation increased with increasing mutation rate (Fig. 2f).
