PACO: a Shiny app for comparing perturbed pathways associated with different phenotypes

Motivation: Pathways are biological networks describing interactions between genes, proteins, non-coding RNAs, drugs and chemical compounds that contribute to develop a specific metabolic function or biological process. Identifying perturbed pathways associated with a phenotype or condition helps to understand how functional processes are altered in complex diseases and which genes play a key role in these alterations. Recently, several algorithms have been developed to identify perturbed pathways associated with a phenotype. Still, no tools are available to visualize and compare perturbed pathways in the same species or different organisms. Results: Here, we present a web app called PAthway COmparator (PACO) to compare two or more sets of altered pathways associated with different phenotypes, starting from either custom data or simulation data returned by the pathway analysis algorithms MITHrIL and PHENSIM. The app allows users to visualize and compare the altered pathways, and zoom into specific regions. We show the potential applicability of PACO through a case study in which perturbed immune system pathways are compared in mice and humans after up-regulation of Interferon-stimulated gene 15 (ISG15).