Figure 1.
Paxtools can be used to obtain pathway data from different sources and use the data to answer a wide range of biological questions.
Paxtools facilitates working with pathway information by removing technical barriers and acts as a common development platform for other tools and algorithms.
Figure 2.
A plausible signaling path (yellow) between the androgen receptor (AR, top) and the TP53 protein (p53, right) is found by a Paxtools “paths-between” query and visualized in the Chisio BioPAX Editor.
These cross-talks are difficult to find manually without a graph search because of the large number of connections to/from AR and p53 and because of fragmentation of data across multiple pathway data sources.
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.