GTEx笔记
网址：https://www.gtexportal.org/home/
官方Q&A：https://gtexportal.org/home/faq
参考文献：https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7737656/
GTEx v8数据来源：
838 donors and 17,382 samples from 52 tissues and two cell lines
【715 (85.3%) were European American,
103 (12.3%) African American,
and 12 (1.4%) Asian American,
with 16 (1.9%) reporting Hispanic or Latino ethnicity;
557 (66.4%) donors were male and 281 (33.5%) female 】
数据类型
RNA-seq，WGS
数据下载地址
https://gtexportal.org/home/datasets
QTL
表达数量性状基因座（expression Quantitative Trait Loci,eQTL）是对上述概念的进一步深化，它指的是染色体上一些能特定调控mRNA和蛋白质表达水平的区域，其mRNA/蛋白质的表达水平量与数量性状成比例关系。eQTL可分为顺式作用eQTL和反式作用eQTL，顺式作用eQTL就是某个基因的eQTL定位到该基因所在的基因组区域，表明可能是该基因本身的差别引起的mRNA水平变化；反式作用eQTL是指某个基因的eQTL定位到其他基因组区域，表明其他基因的差别控制该基因mRNA水平的差异。
sQTL：剪接数量性状基因座
ieQTL：细胞类型-相互作用eQTL
isQTL：细胞类型-相互作用sQTL
Why is the effect size direction of some eQTLs opposite to that reported elsewhere?
The effect sizes of eQTLs are defined as the effect of the alternative allele (ALT) relative to the reference (REF) allele in the human genome reference. In other words, the eQTL effect allele is the ALT allele, not the minor allele.
How should eQTL effect sizes be interpreted?
The portal displays two values that are related to the eQTL effect sizes:
Allelic fold-change (aFC), a measure of cis-eQTL effect size, is defined as the log-ratio between the expression of the haplotype carrying the alternative eVariant allele to the one carrying the reference allele in log2 scale. Currently, due to computational limitation, only the aFC of the most significant variant of each eGene is available.
Normalized effect size (NES), previously known as the effect size on the portal, is defined as the slope of the linear regression, and is computed as the effect of the alternative allele (ALT) relative to the reference allele (REF) in the human genome reference (i.e., the eQTL effect allele is the ALT allele). NES are computed in a normalized space where magnitude has no direct biological interpretation.
eVariant: a significant variant associated with an eGene.
Why are there different number of tissues available on the Single-tissue eQTL page?
（关于significant cutoff的定义）
The "Single-Tissue eQTLs" section allows you to look up cis eQTLs which have been precomputed in a +/- 1Mb cis window around the transcription start site (TSS). Significance was determined using a Q-value threshold. At least 70 samples per tissue are necessary to achieve the statistical power needed for this type of analysis.
In contrast, the "GTEx eQTL Calculator" and GTEx eQTL Dashboard allow you to compute, on demand, an association between a SNP and gene of your choice. The association may be cis or trans. This calculation may be performed in tissues for which we have more than 10 samples. No Q-value filtering is performed and the user is left to interpret the significance of the p-value.
Single Cell Expression Data Coming soon!芜湖~
