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The blastall program was used to align each platform's probe sequences to local transcript databases.
In contrast to previous work (Taylor et al., 2010), we did not see any significant correlation with local transcript expression of RARS2 or RNGTT and deletions at MAP3K7 locus (see below).
The DBIRD complex functions at the interface between core mRNP particles and RNAPII, affecting local transcript elongation rates and alternative splicing; it is possible that the RNA-binding domain of DBC1 may have a key role on this function.
In mature tissues, where cells no longer move nor enlarge irreversibly, the transcriptional regulation of gene expression (for example environmental induction) is revealed by the temporal derivative of local transcript density.
In a span of 25 codons, it contains 21 codons whose regulation can be linked to Trm4 (UGU) and Trm9 (AGA, GAA, and AAG), thus representing a local transcript region that is predicted to be highly dependent on specific tRNA modifications for translation.
For an integrative analysis – combining copy number and gene expression data – we selected features displaying linear correlations between CN state and local transcript expression levels, to identify genome-wide expression quantitative trait loci (eQTL) in the discovery data set (see Methods).
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Our study suggests that T2D SNPs have broad-reaching and tissue-specific effects that often extend beyond local transcripts and raises the question of whether patterns of cis or trans transcript regulation are a key feature of the architecture of complex traits.
All of these studies consistently showed the CAD risk variants in the Chr9p21 region were associated with ANRIL expression and have very little effect on the other local transcripts.
This involved the development by two independent analysts of an initial coding framework capturing the overarching and related sub-themes within the local language transcript, which was then synthesised through discussion with modification or addition of codes until theoretical saturation was obtained.
The local Oromiffa transcripts were then translated into English by the first author (ST), who is a psychiatrist, and the accuracy of the translations was cross-checked by the coauthor (TS), a psychiatrist who has good command of both languages.
In both studies, there was no effect of either local G/C content, transcript abundance, used as a proxy for gene expression, or timing of replication on the local mutation rate.
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