In most gene expression studies, alterations of expression levels are expressed in relation to the simultaneously determined expression level of a reference sample and conclusions are drawn based on these ratios.
Third, all miRNAs may not be able to result in phenotypic changes on their own; their effect may be context specific and may need to be coupled with alterations of expression of either other miRNAs or mRNAs to alter phenotype.
Since CGD neutrophils inhibited conidial growth as efficiently as normal neutrophils, we first focused on the identification of common genes that showed alterations of expression in the presence of either normal or CGD neutrophils.
The algorithm for calculating the percentage of alterations of expression profile gene and percentage of expression frequency for each Vβ gene were performed as described in the legend to Fig. 3A.
Noteworthy, inducible short-time overexpression of RBPs could be beneficial to measure direct effects of proteins on gene expression by minimizing secondary effects that may raise after prolonged alterations of expression levels (Scherrer et al., submitted).
Thus, in order to avoid false/erroneous classification of miRNAs as up- and down- regulated in mucosal biopsies of IBD patients, only miRNAs with alterations of expression that fitted stringent thresholds (2−ΔΔCT>5-fold and 2−ΔΔCT<0.2-fold, respectively) were considered.
