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

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Presentation transcript:

Modeling Functional Genomics Datasets CVM Lessons 4&5 10 July 2007Bindu Nanduri

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

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

Networks and pathways

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

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

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

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

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

KEGG BioCyc Reactome GenMAPP BioCarta TransPATH international.com/pages/index.php?id=transpathda tabases Pathguide – the pathway resource list Available resources

Network Topology (PPI)

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

Ingenuity Pathway Analysis PathwayStudio PathwayArchitect Cytoscape Biological Networks GeneGO

Nanduri etal (unpublished)

GO term enrichment Nanduri etal (unpublished)

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