This notebooks outlines the process of generating unbiased candidate mechanisms and comparing them to the dogmatic mechanisms from the NeuroMMSig Database.
This notebook demonstrates the utilities in PyBEL Tools that facilitate the exploration and expansion of subgraphs to allow for easier interpretation and contextualization of their underlying mechanisms. The data used in this notebook comes from the AETIONOMY Alzheimer's Disease (AD) knowledge assembly that has been annotated with the NeuromMMSig Database.
This notebook explores methods of comparing subgraphs and identifying meaningful overlaps between them.
This notebooks demonstrates the usage of a variant on the Network Perturbation Amplitude algorithm to analyze an BEL knowledge assembly in the context of a differential gene expression experiment.
This notebook compares the candidate mechanism perturbation amplitude at multiple disease stages in Alzheimer's Disease experiments, using the PyBEL web service.
This notebook calculates the concordance between differential gene expression and the causal relationships between their protein products. This analysis assumes the forward hypothesis, under which gene expression is believed to be correlated with protein activity.