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Such differing study setting may not necessarily have the power to detect the previously observed genetic associations, involving approximately 550 and 200 cases and controls, respectively, and stringently selected for their genetic homogeneity (at least three generations from mainland France) (Oliveira et al. 2014a, b, c).
A more stringently selected cohort may have been more responsive.
Our study clearly demonstrates that a stringently selected shRNA-library is well suited for the unbiased identification of novel potent and non-toxic shRNAs in addition to those predicted by commonly used public algorithms.
We chose to calculate two separate datasets using SAM (one not stringent, and one stringent) to circumvent the issues that a stringently ascertained dataset might miss relevant pathways (because too few genes are entered in the analysis) or that a larger, less stringently selected set of genes would contain too many false positives.
Those patients had been stringently selected for trastuzumab treatment primarily by FISH (90%).
Thus, even in our stringently selected fibroblast samples and gene set, topology remains evident in the gene expression profile.
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First, we confirmed the influence of Toxoplasma infection in BD by analysing a much larger sample than in a previous study (Table 1) and also by stringently selecting those born in France for sample homogeneity (Hamdani et al. 2013).
To stringently select isolated promoters and intergenic regions shown in (A ) and attribute their putative enhancer and control promoter status, a threshold was defined (in dashed green line).
Thus, to stringently select for compounds that represent biologically relevant hits with respect to the phenotypic screen used, all 112 autofluorescent compounds were excluded from further analysis, identifying three hits from a primary screen of 6,764 molecules (Fig. 3B).
When there exist a very large number of SNPs to choose from it would be possible to stringently select SNPs with high FSV, large number of covering reads and a high proportion of non-reference reads.
To most stringently select for candidate CS/CPB-regulated genes, we applied multiple testing correction, and identified 916 differentially regulated transcripts (P<0.01, after standard Bonferroni correction).
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