Analysis framework and experimental design for evaluating synergy-driving gene expression.

ABSTRACT: The mechanisms by which genetic risk variants interact with each other, as well as environmental factors, to contribute to complex genetic disorders remain unclear. We describe in detail our recently published approach to resolve distinct additive and synergistic transcriptomic effects after combinatorial manipulation of genetic variants and/or chemical perturbagens. Although first developed for CRISPR-based perturbation studies of isogenic human induced pluripotent stem cell-derived neurons, our methodology can be broadly applied to any RNA sequencing dataset, provided that raw read counts are available. Whereas other differential expression analyses reveal the effect of individual perturbations, here we specifically query interactions between two or more perturbagens, resolving the exten

SUBMITTER: Schrode N 

PROVIDER: S-EPMC8609447 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature