To summarize, our study indicates that along with significant overlap, there are also profound differences between results oflocalandcis-eQTL mapping approaches, such that these should be considered complimentary methods of assessing potentialcis-regulation of gene expression. We believe that our data sho...
Notably, we find significant eQTL for nearly every gene in our analysis, which include all but very lowly expressed genes (less than 1 cpm in more than 50% of samples). The wide discovery of eQTL is potentially beneficial for analyses utilizing these results, such as colocalization analysis...
For example, we observed that the iPSC-PPC-unique singleton egQTL in the CDC37L1-DT locus overlapped an active promoter region in the adult islet, while in both adult islet and adult whole pancreas, the variants in the same region are not active (Fig. 3d). Overall, these results show ...
Supplementary Figure S10 shows the power comparison results based on gene C3orf22 under Uni-directional effects and Bi-directional effects with noise to eQTL. We can see that the powers of these tests based on corrected LD structure perform better than those based on uncorrected LD structure ...
Donor eyes were dissected for each tissue from the macula region and from the periphery away from the macula (non-macula; Figure 1A), resulting in a total of 529 human samples of four different tissue and region types (see STAR Methods). As expected, we observed distinct gene expression ...
Manhattan plots displaying genetic association results for 489 related individuals from the Val-de-Marne sample using a linear mixed model approach implemented in GEMMA software (A) The IFNγ-BCG phenotype across 117354 SNPs in the chromosome 8 region from 61 Mb to 91.5 Mb, and (B) The...
Consistent with our results, three previous analyses discussed MATALPHA1 as a regulator for genes in this eQTL module, and Lirnet additionally suggested MATALPHA2 and TBK1. As these candidate regulators lie in cis to this eQTL hotspot region, the genetic variation in this region may directly ...
The gene set enrichment analysis for candidate genes was conducted using g:Profiler [61]. The significance of GO terms was determined by the pre-adjusted threshold (p < 0.05) in g:Profiler. 4.8. Enrichment of Cis-eQTLs in GWAS Hit Regions From our previous GWAS results [17], we first ...
Density plots show the position of all miR and isomiR-eQTL (FDR < 0.05) in the genome (Figure 2C andFigure 3C).Figure 2D andFigure 3D represent the number of unique miRNA precursors found in BRCA and PRAD studies, respectively. These results indicate that SNPs may impact miRNA processing ...