Since we observed inductions in MCT and deviations in the expression of MyHC isoforms, major components of the contractile apparatus, after SC depletion and SNT, we measured ex vivo muscle contractility of Ctrl and P7DTA EDL muscles.
As indicated in the previous section, for each sample we can calculate the deviation in expression against the estimated expression values calculated for each specific gene-exon pair by applying a linear regression model to the data.
Recently, we argued that sporadic Parkinson's be fundamentally characterized as a pathological deviation from normality in the expression program of a cell, the PD-state.
Does the deviation in gene expression between the two sets of tumors result from an early transgenic STAT5 effect, or does continuously deregulated STAT5 expression in the tumors govern the gene-expression profile?
The epistatic effect of two GSTFs X and Y on the expression of a gene i was measured as the deviation between the expression change observed in the double mutant M xΔyΔi and the expression change expected given the single mutants M xΔi + M yΔi (ε txpn, XYi = | M xΔyΔi − (M xΔi + M yΔi )|).
The effect of a genetic interaction between two GSTFs X and Y on a gene i can be measured as the deviation between the expression change observed in the double mutant M xΔyΔi and the expected expression change, given each single mutant M xΔi + M yΔi (ε txpn,Xyi = |M xΔyΔI − (M xΔi + M yΔi )|).
To assess the extent to which this phenomenon explains the deviation in expression ratios observed across the whole set of targets on the chip, we undertook an alternative analysis.
Supplementary material Fig. S3A shows the standard deviation of all genes in the expression data.
Because the variance in read counts is in part a function of transcript length [ 65], we calculated the standard deviation in differential expression as a sliding window of the 500 closest genes in terms of transcript length.
The d/a ratio (Eq. 1) was used to quantify the level of deviation in transcript expression of SRG150 relative to the midparent value of SRG100 and SRG200 [ 26] for any genes with FPKM > 1 in SRG100, SRG200, or SRG150.
