PathwayAnalysisBlauBook

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1. Pathway analysis

Example A: Pathway visualization

• Visualizes gene expression data from Lesch Nyhan Disease patient on the Purine metabolism pathway from WikiPathways
• Dataset: GSE24345
• Pathway: https://www.wikipathways.org/instance/WP4792
• R script

Example B: Pathway enrichment analysis

• Identifies affected pathways in dataset
• Dataset: GSE24345
• Pathway collection: WikiPathways human pathway collection
• R script

2. Network analysis

Example A: Network Extension

• Extends the Purine metabolism pathway from WikiPathways with known drug-target interactions from DrugBank
• Pathway: https://www.wikipathways.org/instance/WP4792
• Drug-target database: DrugBank (https://www.drugbank.ca/)
• R script

3. Linking chemical (biomarker) data with RDF

Prerequisits: Beginners tutorial on SPARQL

• Provides basic explanation on RDF, SPARQL and building queries.
• Follow the tutorial here.

Example A: Mapping chemical IDs with BridgeDb

Example B: Performing SPARQL query with InChIKey

Example C: Performing SPARQL query with neutralised InChIKey

Example D: Additiona; SPARQL queries for chemical compounds