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We then investigated pathway enrichment considering the set of CNVs deemed functional through the association between the corresponding transcript levels and the copy number states and focused on those which also show differentiation across populations.
Additional file 11: Table S7 provides the ten genes with the highest direct correlation values; in addition, the full list of genes with correlation values between the corresponding transcript and volatile levels is included in the supplementary data (Additional file 8: Table S5).
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Linkage between regulated genes and the corresponding transcript quantities highlights tumor over-expressed transcripts as preferred targets for identifying hyper-splicing signatures [16].
(B) Left panel: normalized ratio between enzymatic activity and the corresponding transcript levels.
When comparing the coregulation between the protein and the corresponding transcript, extracted from Table 1, it was found to be low (13%).
Each row corresponds to an enzymatic activity summarizing (A) Left panel: normalized ratios between enzymatic activities and the corresponding transcript levels (same as Figure 2 ), Right panel: significance levels of differences in these ratios between the reference condition (YPA) and the other time points.
For the tumor tissue samples, the correlation between DNA methylation levels and the corresponding transcript abundance, for the 758 CpG sites with significant variation in methylation across tumors, was also negative, but much weaker (Figure 4B, mean ρ = −0.08).
Probes were designed to hybridize between exons to ensure the detection of the corresponding transcript avoiding genomic DNA amplification.
n.d., the corresponding transcript was non-detected.
We observed that there was no statistically significant connection between Htz1 and Nap1 binding and the corresponding transcripts.
In line with Alu exon-induced transcript degradation, we observe a correlation between Alu exon inclusion and downregulation of the corresponding transcripts in the HNRNPC knockdown.
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