This analysis shows that several biological processes were overrepresented among gene targets of these miRNAs: regulation of transcription, development and differentiation, ubiquitin cycle, signal transduction, transport, and tumor suppression (synonym category: regulation of progression through cell cycle) (FDR p<10−9).
Here, we focus on the 42 upregulated genes in the category regulation of apoptosis.
Within the category "regulation of leukocyte activation," ephrin B1 was downregulated, and we therefore examined all ephrins and their receptors.
We found that CHH modifications are highest in the introns of genes in the GO category "regulation of transcription" for both AHB and EHB.
The exception is the GO category, regulation of gene expression, epigenetics, in which the few genes that were detected were only found in exfoliated cells.
Finally, 62 upregulated genes belonged to the category cell motility, in which 22 of the genes related to inflammatory response or antigen presentation (data not shown) while 42 upregulated genes were in the category regulation of apoptosis.
To determine the central genes in this module, we identified the hub genes involved in a representative GO category; "Regulation of synaptic transmission" by mapping the connectivity amongst genes within this category (Fig. 7b).
As an illustration of the strength of this effect, the GO category "regulation of transcription, DNA-dependent" contains 1224 genes with a z GO of -8.893 (p = 10-18) for the mouse-human species pair, and for the cow-dog species pair the category has a z GO of -7.182 (p = 10-12).
These shared genes could be divided in four main categories: regulation of cell cycle progression and proliferation (ex.
These genes cluster into 5 major categories: regulation of transcription, transport, signal transduction, protein turnover, and metabolism.
