Computational Assessment of the Expression-modulating Potential for Non-coding Variants  

作　　者：Fang-Yuan Shi Yu Wang Dong Huang Yu Liang Nan Liang Xiao-Wei Chen Ge Gao 

机构地区：[1]State Key Laboratory of Protein and Plant Gene Research,School of Life Sciences,Biomedical Pioneering Innovative Center(BIOPIC)&Beijing Advanced Innovation Center for Genomics(ICG),Center for Bioinformatics(CBI),Peking University,Beijing 100871,China [2]State Key Laboratory of Membrane Biology,Institute of Molecular Medicine,Peking University,Beijing 100871,China [3]Human Aging Research Institute,School of Life Science,Nanchang University,Nanchang 330031,China [4]Peking-Tsinghua Center for Life Sciences,Academy for Advanced Interdisciplinary Studies,Peking University,Beijing 100871,China

出　　处：《Genomics, Proteomics & Bioinformatics》2023年第3期662-673,共12页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by funds from the National Key R&D Program of China(Grant No.2016YFC0901603);the National High-tech R&D Program of China(Grant No.2015AA020108);as well as the State Key Laboratory of Protein and Plant Gene Research and the Beijing Advanced Innovation Center for Genomics(ICG)at Peking University;supported in part by the National Program for Support of Top-notch Young Professionals。

摘　　要：Large-scale genome-wide association studies(GWAS)and expression quantitative trait locus(eQTL)studies have identified multiple non-coding variants associated with genetic diseases by affecting gene expression.However,pinpointing causal variants effectively and efficiently remains a serious challenge.Here,we developed CARMEN,a novel algorithm to identify functional non-coding expression-modulating variants.Multiple evaluations demonstrated CARMEN’s superior performance over state-of-the-art tools.Applying CARMEN to GWAS and eQTL datasets further pinpointed several causal variants other than the reported lead single-nucleotide polymorphisms(SNPs).CARMEN scales well with the massive datasets,and is available online as a web server at http://carmen.gao-lab.org.

关 键 词：Non-coding variant Expression-modulating variant Gene regulation Algorithm Web server 

分 类 号：R394[医药卫生—医学遗传学]