Using Biological Pathway Data with Paxtools
Figure 3
A Sif (Simple Interaction Format) rule reduces mechanistic BioPAX interactions (left column) to simpler binary interactions (right column) based on the pattern defined in the rule.
Different rules should be used dependent on the biological question at hand. For example a State Change interaction is inferred when the rule detects phosphorylation of p53 by p38. This is a useful relationship that can be applied to protein signaling cascade analysis from proteomics data. “Sequential Catalysis” rule on the other hand links entities that are responsible for catalyzing subsequent reactions. This is a relationship that frequently occurs in metabolic pathways and is useful for metabolomic studies where changes in the concentration of substrates are observed.