User Guides
In this tutorial, we introduce the end-user to a pathway network that describes the activation of transmembrane receptors in macrophages and their downfield signal transduction pathways linked to inflammation. In the first phase, the user will visualize this network to identify IL1R, a receptor known to promote inflammation, and its two ligands (IL1A and IL1B). In the second phase, the user will run the analysis software using python (within a colab notebook) to identify receptors linked to inflammation through the pathway network. The returned list includes IL1R and its associated pathway, which the user can cross-validate by visual inspection of the network in cytoscape. Additional routines are shown in the notebook, which demonstrate how the user can inspect the mRNA and immunohistochemistry data for each protein within the network that was used to score each inflammatory pathway. Advanced documentation provides details on the algorithm, how to input experimental data including mRNA and mAbs, and how to modify the pathway network.
The following steps should be done in order:
- visualize network (Cytoscape)
- analyse network (Colaboratory)