eQTL databases

[…] ci that contain sequence variants that are found to affect the expression of genes. They are identified by relating gene expression measurements to genotyping information in panels of individuals []. eQTL databases, such as GTEx portal [], provide the opportunity to link GWAS results to the transcriptome level, in which a GWAS hit matching an eQTL for a given gene, brings up the hypothesis that th […]

[…] ghted network analysis was performed where each path through the network was weighted by the strength of the (trans) eQTL of the index-SNP. The eQTL values were calculated using a large collection of eQTL databases with tissues and cells relevant to cardiovascular disease. Like in the unweighted network analysis permutation was used to determine significance threshold. Through this weighted networ […]

[…] peak data, namely DNase-seq peaks of open chromatin, FAIRE peaks of open chromatin, TFBS SPP-based peaks, TFBS PeakSeq-based peaks and Histone peaks. In addition, eQTLs were determined using several eQTL databases, namely eQTL Browser, GTEx and seeQTL. Common networks were identified using GeneMANIA. This database collated data on protein and genetic interactions from a number of sources, includi […]

[…] 0 human brain regions from control individuals, establishing a comprehensive data set for regional specificity of gene expression regulation across human brain.Next, the varying sample sizes of brain eQTL databases can potentially affect the reliability of eQTL analyses. It is known that the power to detect eQTL is partly a function of sample size. Although it was estimated that a sample size of 1 […]

[…] s. These analyses confirm that our approach is capable to pick up every candidate gene that was found to have SNP-dependent expression levels in tissues relevant for IBD. As expected based on the two eQTL databases that were used, not all 4C-seq candidate genes we found to have a SNP-dependent expression pattern. This is (at least in part) due to the highly context-specific nature of SNP-dependent […]

[…] ct on WC and WHR is less evident.We evaluated putative functional significance for each newly-identified locus using the Encyclopedia of DNA Elements (ENCODE) and expression quantitative trait locus (eQTL) databases. Three of these novel SNPs, rs3809128 near CNPY2, rs2057291 at GNAS, and rs3791679 near EFEMP1, were predicted to be functional as they are located either in promoter or enhancer regio […]