FastQTL是一款专门用于cis-eQTL分析的软件,在GTEx项目中就是采用该软件进行cis-eQTL的分析,对应的文章发表在Bioinformatics杂志上,链接如下 https://academic.oup.com/bioinformatics/article/32/10/1479/1742545 源代码保存在sourceforge上,网址如下 http://fastqtl.sourceforge.net/ 该软件具有以下几个特点 运行速度快,...
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。
4. 进行eQTL分析 代码如下 运行完成之后,查看对应的输出结果即可,cis和trans的输出结果是类似的,示意如下 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。 ·end· —如果...
We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using transcriptome data from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (N = 1,981), The Cancer Genome Atlas (TCGA) (N = 458), and the Genotype-Tissue Expression (GTEx) project (N = ...
eQTL analysis, and employed experimental models of early-stage disease to functionally validate the candidate genes we identified. Of 11 confirmed GWAS susceptibility loci identified for ovarian cancer, one contained a statistically significant eQTL association (HOXD9) at a FDR≤0.1. Two additional ...
which was built using the MOLGENIS framework76. We also providecis-eQTL files formatted for use in SMR, MAFs and replication statistics forcis-eQTL,trans-eQTL and eQTSs. Per-cohort summary statistics for discovery cohorts can be made available after approval of an analysis proposal in eQTLGen ...
(SNPs) through an analysis of variance using an additive linear model with the MatrixEQTL package. A permutation analysis then assessed the significance of the best SNPs for each spliced transcript. Functional enrichment analysis was performed on the sGenes to investigate their roles in the immune ...
analysis of F1 data results in a probabilistic description of the role ofcisandtranseffects. However, the use of F1 crosses classifies mechanisms underlying regulatory changes as eithercis- ortrans-acting more accurately than eQTL approaches, because the functional differences in vivo between the two...
It has been shown that the SNP can affect the probe level analysis of gene expression and its effect is related to the position of the SNP on the probe [5], [18]. However, it is not clear whether and how much it affects the probe level eQTL analysis. If the effect is large in pr...
Revealing the architecture of gene regulation: the promise of eQTL studies Trends in Genetics Journal2008, Trends in Genetics Yoav Gilad, ... Jonathan K. Pritchard Molecular studies of gene regulation have classified regulatory interactions based on their effects in cis or trans, and the terms hav...