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In fact, the identified MRs by VIPER are scored based on their exerted effects on their downstream targets in that the more distinction observed in the expression degrees of the MR targets between cases and controls leads to a higher enrichment score demonstrating the higher activity of that MR. Our findings in this study are in line the findings from co-expression network analysis in1.
Behavioral changes in the mdr 1a/1b knockout mice in comparison to the wild-type mice allow for the investigation of P-gp-dependent variations in the expression degrees of the CNS which leads to functional dispositions.
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The obtained hook curve thus describes the 'trajectory' of a pairing of 3′/5-probe sets upon changing expression degree of the respective transcript (see Figure 12a for illustration).
Moreover, the potential dependence of the probe intensities on the degree of degradation gives rise to systematic errors of the estimated expression degree of the transcripts which requires appropriate correction.
In the extraction of TFs and their regulated genes, the TF was also cited from the TRANSFAC database [ 19], but the expression degree of the TF was not considered, due to the small expression changes even under different conditions.
The so-called degradation hook-plot, shown in Figure 1a and b, displays this 3′/5′ intensity difference in dependence on the mean logged probe intensity approximating the expression degree of the respective gene.
This result indicates that the expression degrees of present probe sets located in the mix-, S- and sat-ranges of the original hooks remain, on the average, essentially unchanged after updating the probe sets.
The expression degrees of DCN and FMOD genes in the regenerated tissues were twice or more as large as those in the normal cartilage, and the expression degree of GPC6 gene in the regenerated tissues was quarter as little as those in the normal cartilage.
The expression degrees of COL2A1, COL1A2, and COL10A1 genes in the regenerated tissues were twice or more as large as those in the normal cartilage.
The expression degrees of SPARC, FLOD2, CHAD, CTGF, and COMPs genes in the regenerated tissues were twice or more as large as those in the normal cartilage.
[Sg]target is the (true) expression degree of a selected gene g given as the total concentration of the target transcripts in the hybridization solution independent of their length.
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