Fig 1. Overview of pathway transformation using single sample pathway analysis (ssPA).

A. Pathways are represented as sets of molecules, e.g. genes, proteins, and metabolites. B) Pathway transformation by ssPA facilitates a change of dimension of an omics dataset from a molecular space to a pathway space. C) This transforms a sample-by-molecule expression or abundance matrix to a sample-by-pathway matrix, where values represent the `activity’ of each pathway for each individual sample.