Figure 1. Overview of the APPINetwork package.

Illustration of requirements R packages (blue section), inputs (orange section): databases, UniProt file text of the studied organism and lists of proteins of interest, workflow (green section) and outputs (yellow section): all files that APPINetwork provides to the user. The “new proteins” in the green section are proteins newly identified by APPINetwork as playing a role in the biological process of interest. The “lists of proteins” in the yellow section are the lists of all proteins that make up each sub-network potentially associated with a biological process.