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It should be noted, however, that for the kind of highly modular (i.e. fully interconnected) developmental regulatory networks analyzed here, complexity is not only defined in terms of the number of TRs, but mainly in terms of the density of regulatory interactions and the coupling pattern of feedback structures.
The 5′ UTR shows an intermediate proportion of singletons, 67.8%, perhaps reflective of greater constraint due to a higher density of regulatory elements.
In fact, exonic regions with high density of regulatory motifs have been linked to regions of low SNP density [ 14], low synonymous SNP density [ 15], and negative selection against synonymous substitutions [ 16- 18].
Position effects are not unexpected in light of the density of regulatory elements in the genome (Bernstein et al., 2012) and the long-range action of enhancers (Ellingsen et al., 2005; Ruf et al., 2011).
Although the 1 kb upstream region may contain the highest density of regulatory elements it does not contain all of them, they can be spread throughout the gene and its 3' region as well as going tens to hundreds of kilobases upstream.
Secondary molecular objectives are the T cell activity in the resected tumor specimen, the density of regulatory T cells, and the frequency of tumor reactive T cells in blood and bone marrow in correlation with changes in the level of proteins involved in immune response or angiogenesis and transcriptomics in whole blood cells.
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We found that a higher relative frequency of IR is associated with weaker splice sites, genes with overall short intron lengths, higher expression levels and particular densities of regulatory elements.
Still, it is surprising that common values of c emerged despite quite different numbers of time series for each network and different densities of regulatory links in the networks.
There was significantly increased local infiltration of CD8 and CD4 T cells in responders; whereas non-responders showed an increased density of T regulatory cells in the lesions (Daayana et al, 2010).
Extending a previous observation that a specific set of ESSs was able to inhibit intron retention [ 26], we showed that there is an inverse association of the density of these regulatory elements (and also of the ISE GGG) with the frequency of IR.
Almost seven percent of the known human microRNAs are encoded by imprinted domains and nowhere in the genome there is such a high density of small regulatory RNAs as at imprinted domains, some of which comprise more than 50 small RNAs per Mb.
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