第一列为基因ID, 第二列为snp ID, 第三列为基因和SNP之间的距离, 软件默认分析距离1M以内的SNP-Gene对, 第四列为pvalue值。更多用法请参考官方的说明文档。
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。
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 = ...
Identifying additional common variant susceptibility alleles for ovarian cancer will continue to be restricted by sample size for this uncommon cancer type. By using eQTL analysis to interrogate candidate susceptibility loci that are sub-genome-wide significant, we have found evidence for two additional ...
trans-eQTL and eQTSs. Per-cohort summary statistics for discovery cohorts can be made available after approval of an analysis proposal in eQTLGen and with agreement of the cohort PIs; contact corresponding authors for further information. Trait-associated variants were collected from the EBI GWAS ...
在INFO中,包含了GT和DS两个字段的信息,GT表示基因分型的结果,0表示ref allele, 1表示alt allele; DS表示基因剂量。官方推荐使用DS这个字段的信息。 对于VCF文件,需要压缩之后,用tabix软件建立索引,命令如下 bgzip genotypes.vcf && tabix -p vcf genotypes.vcf.gz ...
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· —如果喜欢,快分享给你的朋友们吧— 往期精彩
C. Holmes. Robust linear models for cis-eqtl analysis. PloS one, 10(5):e0127882, 2015.Rantalainen M, Lindgren CM, Holmes CC. Robust Linear Models for Cis-eQTL Analysis. PloS one. 2015; 10(5):e0127882. Epub 2015/05/21. https://doi.org/10.1371/journal.pone.0127882 PMID: 25992607...
Perform cis-eQTL analysisChaitanya R. Acharya
Finally, we performed a cis-eQTL analysis on human cell lines experiencing ER stress to identify cis-eQTLs that regulate the variable ER stress response. The majority of these cis-eQTLs are unique to a given condition: control or ER stress. Some of these stress-specific cis-eQTLs fall within...