1. Modeling Functional Genomics Datasets CVM8890-101 Lessons 4&5 10 July 2007Bindu Nanduri

2. Lesson 4: Introduction to pathways analysis. Theory and strategies for pathway analysis modeling in different species.

3. Lesson 5: Tools for pathway analysis. Ingenuity, Pathway Studio, etc.

4. Networks and pathways

5. A network is a collection of interactions Pathways are a subset of networks All pathways are networks of interactions not all networks are pathways

6. Young et. al: Transcriptional Regulatory Networks in Saccharomyces cerevisiae; Science 2002

7. A network is a collection of interactions Pathways are a subset of networks All pathways are networks of interactions, however not all networks are pathways! Pathway is a biological network that corresponds to a specific physiological process or phenotype

8. Biological pathways Biological components interacting with each other over time to bring about a single biological effect Pathways can be broken down sub-pathways Some common pathways: signal transduction metabolic pathways, gene regulatory pathways Entities in one pathway can be found in others

9. 3 types of interactions that can be mapped into pathways protein (enzyme) – metabolite (ligand) metabolic pathways metabolic pathways protein – protein cell signaling pathways, protein complexes protein – gene genetic networks

10. KEGG http://www.genome.jp/kegg/ BioCyc http://www.biocyc.org/ Reactome http://www.reactome.org/ GenMAPP http://www.genmapp.org/ BioCarta http://www.biocarta.com/ TransPATH http://www.biobase- international.com/pages/index.php?id=transpathda tabases Pathguide – the pathway resource list http://www.pathguide.org/ http://www.pathguide.org/ Available resources

11. Network Topology (PPI)

12. Network analysis and visualization tools Databases for analysis Text mining algorithms (e.g., natural language processing (NLP)) technologies Expert human curation

13. Ingenuity Pathway Analysis http://www.ingenuity.com/products/pathways_analysis.html PathwayStudio http://www.ariadnegenomics.com/products/pathway-studio/ PathwayArchitect http://www.selectscience.net Cytoscape http://www.cytoscape.org/ Biological Networks http://biologicalnetworks.net/ GeneGO http://www.genego.com/

14. Nanduri etal (unpublished)

15. GO term enrichment Nanduri etal (unpublished)