cis和trans本质上就是通过SNP位点和gene之间的距离进行区分,首先对所有的SNP-gene对进行计算,然后根据距离阈值将结果进行拆分,小于阈值的SNP-gene对归于cis-eQTL, 大于阈值的归于trans-eQTL。
下图所示的为trans-eQTL: 在完全不同基因上 3) 核实测定该基因probe的完整性: 4) 核实所得的结果:probe的辩识性(Identity)达到99.6%,较好 5) 数据集的数据质量检测/分布情况: 6) Mapping:推荐Haley-Knott Regression 和 GEMMA 一起使用,得到更好的结果 7)Mapping后得到 QTL 图谱 灰色的横线:建议的LRS, p-...
H.B. and M.Swertz created the website to host results. H-J.W., M.J.B. and P.D. contributed equally to this work. The BIOS Consortium contributed the subset of whole-blood data used in discovery analyses. The i2QTL Consortium contributedtrans-eQTL and eQTS replication analyses of ...
The results showed that collectively only a very small proportions (2.85%) of the QTL peaks obtained from the SNP-free probes of the SNP-containing probe sets are cis-eQTLs while a much larger proportion of the eQTL peaks (up to 30%) obtained from the SNP-containing probes in the same ...
Trans-pQTLmetQTLA genome-wide association study (GWAS) correlates variation in the genotype with variation in the phenotype across a cohort, but the causal gene mediating that impact is often unclear. When the phenotype is protein abundance, a reasonable hypothesis is that the gene encoding that ...
transcription factors. Most cis-sQTL effects were found in intronic regions, with 27 sQTL variants associated with disease susceptibility and resistance in cattle. Key sGenes identified, such asGSDMA, NLRP6, CASP6, GZMA, CASP4, CASP1, TREM2, NLRP1, andNAIP, were related to inflammasome ...
(that is,trans-eQTL associations). Also, this study was based on eQTL analysis in tumour tissues. Somatic genetic heterogeneity could mask the presence of eQTL associations; but it may also be that genes influence tumour development at early stages of neoplastic development requiring eQTL analysis ...
QTL interval, suggesting that theSWS1expression is potentiallycis-regulated. Additionally, this QTL has the largest effect onSWS1expression, accounting for 31.65% of the variance in F2expression. The two QTLs on LG14 (LOD = 6.62) and LG20 (LOD = 8.58) aretransQTL explaining 9.8 ...
we prioritized several SNPs for validation studies. Notably, the associations of these candidate SNPs with LOAD risk remain to be determined. In future studies, a larger sample size may allow conduction of transcriptomic and chromatin accessibility QTL/eQTL mapping to determine colocalization with GWAS...
“Material and methods”). We were able to detect atrans-effect for 6.6% of control and 9.3% infected condition non-cis local-eQTLs (727 and 1019trans-eQTLs with FDR < 0.05 in control and infected conditions, respectively) (Fig.4f). However, due to the restricted number of available...