biostudies-literatureYang FNIA NIH HHSNIEHS NIH HHSNIMH NIH HHSNCI NIH HHSNational Institutes of HealthNIH HHSNIGMS NIH HHS2513-2520https://www.ebi.ac.uk/biostudies/studies/S-EPMC8428610biostudies-literatureUnknown37(17)<h4>Motivation</h4>Trans-acting expression quantitative trait loci (eQTLs) collectively explain a substantial proportion of expression variation, yet are challenging to detect and replicate since their effects are often individually weak. A large proportion of genetic effects on distal genes are mediated through cis-gene expression. Cis-association (between SNP and cis-gene) and gene-gene correlation conditional on SNP genotype could establish trans-association (between SNP and trans-gene). Both cis-association and gene-gene conditional correlation have effects shared across relevant tissues and conditions, and trans-associations mediated by cis-gene expression also have effects shared across relevant conditions.<h4>Results</h4>We proposed a Cross-Condition Mediation analysis method (CCmedBioinformatics (Oxford, England)CCmed: cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression.PMC8428610F31CA2395572R01GM108711R01 GM108711F31 CA239557R35 ES028379R01 MH110531R01 AG063175U24 CA210999R01 MH116281U24 CA210993SUB-U24 CA2109993R01 CA229618R01 MH106575Duan JGleason KJChen LSHe XWang JYang FPierce BLfalseCCmed: cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression.<h4>Motivation</h4>Trans-acting expression quantitative trait loci (eQTLs) collectively explain a substantial proportion of expression variation, yet are challenging to detect and replicate since their effects are often individually weak. A large proportion of genetic effects on distal genes are mediated through cis-gene expression. Cis-association (between SNP and cis-gene) and gene-gene correlation conditional on SNP genotype could establish trans-association (between SNP and trans-gene). Both cis-association and gene-gene conditional correlation have effects shared across relevant tissues and conditions, and trans-associations mediated by cis-gene expression also have effects shared across relevant conditions.<h4>Results</h4>We proposed a Cross-Condition Mediation analysis method (CCmed2021-01-01T00:00:00Z2021 Sep2025-04-21T18:58:18.568Z2025-02-18T23:32:27.257ZS-EPMC84286103364792810.1093/bioinformatics/btab139