Learning gene networks under SNP perturbation using SNP and allele-specific expression data.

ABSTRACT: Allele-specific expression quantification from RNA-seq reads provides opportunities to study the control of gene regulatory networks by cis-acting and trans-acting genetic variants. Many existing methods performed a single-gene and single-SNP association analysis to identify expression quantitative trait loci (eQTLs), and placed the eQTLs against known gene networks for functional interpretation. Instead, we view eQTL data as a capture of the effects of perturbation of gene regulatory system by a large number of genetic variants and reconstruct a gene network perturbed by eQTLs. We introduce a statistical framework called CiTruss for simultaneously learning a gene network and cis-acting and trans-acting eQTLs that perturb this network, given population allele-sp

SUBMITTER: Yoon JH 

PROVIDER: S-EPMC10634764 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature