Contents

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 isnโ€™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.