Similar to what is observed in Arabidopsis thaliana, vertebrates have differing sets of overlapping genes (i.e. non-conserved) across different species, subsequently leading to high proportion of overlapping pairs of genes containing an LSG [ 69].
Interestingly, parallel rankings of functional categories were found between alternatively spliced genes and DEGs because of the high proportion of overlaps between these two gene sets.
To ensure the data quality, we searched for studies that have a well-defined phenotypic description for PrCa, have a sample size around 100 or more, and have preferably been measured using similar platforms in order to obtain a high proportion of overlapping genes.
For human and mouse, overlap of protein sets among these databases does not equate to a high proportion of overlapping PPIs: most interactions are unique to a single database.
The higher proportion of overlapping genes in fly might be partly explained by the high gene density and the extended UTR length (Additional File 1).
The importance of replicatory compression is further supported by the fact that the shorter genomes also have a higher proportion of overlapping genes and a reduced fraction of non coding DNA.
A total of 2,008 sequences were used – 1,390 conopeptide superfamily sequences and 1,931 for their classes (a high proportion of which overlap).
However, the highest proportions of overlap occurred between brain regions (35.8-71.7%).
Both Dichaete and SoxN show high overlap with CRMs from all three sources, with a high proportion of CRMs overlapping both Dichaete and SoxN binding intervals (Table 2).
This is actually what we observe, as contrasts performed on the same genetic background (Table 1) [4], [6], [13] [13] have a high proportion of significant overlaps (Table 2) independent of whether the same traits or different traits are considered.
