# 1 Overview of PhenoPath

## 1.1 The PhenoPath model

PhenoPath models gene expression expression $$y$$ in terms of a latent pathway score (pseudotime) $$z$$. Uniquely, the evolution of genes along the trajectory isn’t common to each gene but can be perturbed by an additional sample-specific covariate $$\beta$$. For example, this could be the mutational status of each sample or a drug that each sample was exposed to.