WikiPathways

Step 1: Identify the pathway associated with the disease of interest.

Step 2: Analyze the pathway diagram to identify key regulatory nodes.

Step 3: Research genes/proteins at these nodes to identify potential drug targets.

Step 4: Validate targets using experimental data and literature review.

Step 1: Identify the known targets of the drug.

Step 2: Locate pathways containing these targets in WikiPathways.

Step 3: Analyze how the drug's interaction with these targets affects the pathway.

Step 4: Predict downstream effects based on pathway topology.

Step 1: Obtain gene expression data from an experiment.

Step 2: Map differentially expressed genes to pathways in WikiPathways.

Step 3: Perform pathway enrichment analysis to identify significantly altered pathways.

Step 4: Visualize the expression data overlaid on pathway diagrams.

Step 1: Identify pathways known to be involved in the disease.

Step 2: Explore interconnected pathways to identify potential links.

Step 3: Examine the function of genes/proteins within these pathways.

Step 4: Propose novel mechanisms based on pathway interactions and gene functions.

Step 1: Select a relevant pathway for modeling.

Step 2: Obtain kinetic parameters for pathway reactions from literature.

Step 3: Build a mathematical model of the pathway.

Step 4: Simulate the model and validate against experimental data.