今天,我们以deCODE数据库血浆蛋白组的蛋白与GWAS Catalogue数据库的皮肤癌数据为例,介绍pQTL与GWAS之间的共定位分析。其他来源的pQTL也都可以参考此方法进行。首先我们进行数据下载:GWAS数据从GWAS Catalogue网站下载; 网站链接: ebi.ac.uk/gwas/download deCODE血浆蛋白组数据从网站填写申请下载。 网站链接: download....
这些表明sQTL可能是重要且复杂的机制,GWAS相关变体通过该机制影响性状。(这一部分研究相对于eQTL少得多,不太被人关注)查了下,有两个数据库可能有用:eQTL Catalogue(剪接数据比较专用),QTLbase(各种qtl) 1.3 关于tfbs的部分略 1.4 调控区域活性检测(看不懂没意思) CAGE能够确定TSS的确切位置以及基因的表达水平,可...
whereas rs11556924, rs17400325 and rs3922468 were associated with traits that may affect pubertal timing (birth weight, height, and bone mineral density). Ten variants were not previously associated with any GWAS in the GWAS catalogue, including rs407...
To identify novel loci, we considered index SNPs falling outside 400 kb of a SNP previously associated with one of the following: self-report sleep duration or physical activity from the NHGRI-EBI GWAS catalogue35, CHARGE21and CARe62consortia; an analysis of our accelerometer-measured overall ...
这些表明sQTL可能是重要且复杂的机制,GWAS相关变体通过该机制影响性状。(这一部分研究相对于eQTL少得多,不太被人关注)查了下,有两个数据库可能有用:eQTL Catalogue(剪接数据比较专用),QTLbase(各种qtl) 1.3 关于tfbs的部分略 1.4 调控区域活性检测(看不懂没意思)...
Lastly, plausible functional connections were established between the identified eQTLs and genetic variants reported in the GWAS catalogue. Results: DE analysis revealed 1,048, 284, and 94 mRNA transcripts that exhibited differential expression in response to LDL, small LDL, and...
(GWAS) catalogue17include the Netherlands in their “Country of recruitment” metadata. As well as offering insights into demography and human history, refined population genetic studies are important to identify and adequately control confounding effects in genomic studies of health and disease, ...
tabix-p vcf example.vcf.gz# convert VCF to PLINK# To build PLINK compatible files from the VCF files, duplicate positions and SNP id need to be merged or removed.# remove all duplicate entries.# Catalogue duplicate SNP id:grep-v'^#'<(zcatALL.autosomes.phase3_shapeit2_mvncall_integrated_...
After fifteen years of genome-wide association studies (GWAS) in Parkinson's disease (PD), what have we learned? Addressing this question will help catalogue the progress made towards elucidating disease mechanisms, improving the clinical utility of the identified loci, and envisioning how we can ...
(74%) were included within the TFclass catalogue of human genes encoding TFs [52]. There were 447 TFs from the TFclass catalogue not represented by a motif in our dictionary. Despite this, the dictionary included motifs for TFs from each major DNA-binding domain superclass and class (e.g...