This repository contains the analysis code pipeline to identify single-cell variance eQTL (sc-veQTL) as part of the manuscript "Genetic variants associated with cell-type-specific intra-individual gene expression variability reveal new mechanisms of genome regulation"
In this study, we identified a novel genetic regulation mechanism, where genetic variants affect the variance and dispersion of the intra-individual gene expression independent from mean effects. This list of genes (dGene, i.e., gene with dispersion-eQTL) is enriched in the immune response and interspecies interaction and their cellular dispersion levels are associated with auto-immune disease risk.
Scripts are listed by the order in the methods section of the manuscript:
- The collection and QC of the OneK1K cohort
- Generate intra-individual mean, variance, and dispersion matrix for the gene expression
- The sc- eQTL/veQTL/deQTL association
- Simulation to evaluate the accuracy of dispersion estimation
- Pseudotime inference
- The G x G and G x E interaction test
- Tras- eQTL and veQTL mapping
- Replication analysis in non-EUR (East Asian) cohort
The repository will be updated soon after peer review.
Angli Xue, Seyhan Yazar, José Alquicira-Hernández, Anna S E Cuomo, Anne Senabouth, Gracie Gordon, Pooja Kathail, Chun Jimme Ye, Alex W. Hewitt, Joseph E. Powell. Genetic variants associated with cell-type-specific intra-individual gene expression variability reveal new mechanisms of genome regulation. Under Review. 2024. (Preprint)
For questions, please email us at Angli Xue ([email protected]) or Joseph E. Powell ([email protected])