Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions
Figure 3
Protocol for extraction of a PPI subnetwork related to phosphorylation in Alzheimer's disease.
The flowchart illustrates the input terms and options used to generate a topic-focused PPI subnetwork. Eight genes were selected as a result of an unbiased literature mining query for proteins related to Alzheimer's disease (AD) and phosphorylation (see main text for details). The PPI network of first neighbours of these genes in HIPPIE was generated. Then, filters were applied to focus on a PPI subnetwork or proteins expressed in the brain and related to cell death, thus relevant to AD.