Dorigo, B., Schalch, T., Bystricky, K. & Richmond, T.J. Chromatin fiber folding: requirement for the histone H4 N-terminal tail.
Thus there is a two-fold requirement to study pharmacalogical agents with activity against LINE-1 elements.
Similarly, rare codons (as a proxy of slowly translated regions) were also associated to particular secondary structure elements, which have different folding requirements [ 26, 27].
Determining the sequence of nucleotides that would fold into a given structure is not a trivial problem, due to imperfect thermodynamic rules and additional constraints related to sequence synthesis or three-dimensional folding requirements.
The main reason is three fold: inhomogeneous requirement, function and form definition in the general design context, ill nature of function-to-form mapping and difficulties of design synthesis with qualitative information.
In contrast, the approach of Paul et al. [ 14] consisted of evaluating 8000 genes choosing a 2.5 fold change requirement.
For an exon to be scored significantly different, we set a false discovery rate of <1% and a minimum fold change requirement of two-fold.
In contrast, the functional analysis of the genetic differences between wild and domesticated fish was based on less stringent criteria, with a p ≤ 0.05 and with no fold change requirement and were further analysed in R v.3.0.2 (R Core Team, 2014).
Instead, they fold organizational requirements into the category of routine overhead costs costs that divert precious resources from the real work of delivering programs.
Using this statistical test (specifically, an FDR cutoff of 10−4 and 4-fold change requirement) results in very similar lists of up- and down-regulated genes.
In addition, we screened genes that met a 2-fold change requirement using both statistical methods.
