The suffered mutations are reflected (or not) in a qualitative change of the BR.
The CG representation of each mutant is listed in Appendix table 2; for each mutant, charge mutations are reflected by changing between Q-type and K-type beads at the appropriate point in the sequence.
Since the former mutations are reflected in the mtDNA from buccal cells and the latter mutations in the mtDNA from lymphocytes, the presence of these six mutations could be explained by a single sample-mixing event in the laboratory: contamination of the buccal sample ζ with the buccal sample ε at the amplification step for the "Dloop1" fragment.
Proteins associated with the group "J", involved with translation, ribosomal structure and biogenesis, are dominated by highly conserved ribosomal proteins – and this high level of conservation and intolerance to mutation is reflected in an invariance of pI.
For the purpose of computing RIF, all that matters is that these various multi-scale events set in motion by the MSTN mutation are reflected by a measurable transcriptional change in output DE genes like MYL2.
We performed the same analysis also on monoallelic SNPs: due to the lack of buffering effect, selection is more effective on nonsynonymous mutations and this is reflected by the percentages of high, moderate and low effect substitutions.
The critical role for chromatin-organizing proteins is reflected by frequent mutations, such as the recently described mutation of ARID1A in ovarian cancer [ 47] and other cancers [ 79].
Despite the low bootstrap support, all but the three above-mentioned mutations were free of homoplasy (which is reflected by very high retention and consistency indices in the parsimony analysis, see Figure 3) and can therefore be considered as diagnostic.
This is reflected by, high mutation rates at NRs than at linker regions, which are depleted of nucleosomes [ 9, 25] and could conceivably explain the frequent occurrence of novel TFBSs in these regions.
Finally we addressed the question whether the heterogeneity of the tumor as seen by a pathologist is reflected by different mutation patterns or copy number alterations, e.g. if the localization of the biopsy matters.
