Exact(3)
Attribution of each NP event is determined centrally using two composite attribution rules of different stringency.
Our empirical values of three theta are located within the following ranges: θ = ({ θ1, θ2, θ3} ⊂ ({2.5 ~ 1.5,2.0 ~ 1.0,1.5 ~ 0.5}), where θ1 > θ2 > θ3 is required for implementation of different stringency.
The hybridization mix was washed with wash buffers of different stringency in the presence of magnetic beads (Streptavidin Dynabeads, Life Technologies) at 47°C and the eluate was post-capture PCR amplified (18 cycles) with Illumina PCR primers appropriate to the kit used.
Similar(57)
To select genes from gene sets differentially expressed in EWS-FLI1 knockdown experiments (deltaKD) and in primary ESFT (deltaET) for intersection, we deliberately chose two cut-offs of different stringencies that would allow to maximize the number of genes for functional annotation in GS1 and GS2 at a reasonably significant p-value.
Genes consistently regulated by EWS-FLI1 in cell line models and primary tumors were identified by applying thresholds of different stringencies to the two gene lists (adjusted P-value cutoffs: 0.1 and 0.25, gene sets "GS1" and "GS2", respectively. For details, see Materials and Methods section).
However, the peaks mapped by TAMAL represent a subset of peaks mapped by the permutation algorithm, and were completely contained within the latter set, indicating that the discrepancy in peak number and size is a result of different stringencies set by these algorithms (Supplementary Material, Fig. S3B).
Using the web-interface, these data sets were queried for the number of genes highly expressed in fetal liver or placenta, according to different stringency levels.
The lists of the ORFs considered for each of the metabolic functions, for different stringencies of the criteria (i.e. cut-off in E-values) is presented in Additional file 2, whereas the data presented in Additional file 1 refer to a cut-off E-values of 1E-50.
Author's response: Probably, there are some theories of punctuational evolution based on different rate of mutations or different stringency of reparation processes during evolutionary stasis and during phase of accelerated evolution.
Another advantage of devices using different stringency buffer zones is that they can be of any size or shape.
To estimate the prevalence of NATs in Plasmodium, we established two sets of thresholds with different stringency (see Methods for details).
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