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

Modeling Functional Genomics Modeling Functional Genomics DatasetsDatasets

CVM8890-101CVM8890-101

Lessons 4&5Lessons 4&5

10 July 200710 July 2007 Bindu NanduriBindu Nanduri

Lesson 4: Introduction to Lesson 4: Introduction to pathways analysis. Theory pathways analysis. Theory and strategies for pathway and strategies for pathway

analysis modeling in different analysis modeling in different species.species.

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

Studio, etc. Studio, etc.

Networks and pathways

A network is a collection of interactionsA network is a collection of interactions

Pathways are a subset of networksPathways are a subset of networks

All pathways are networks of interactionsAll pathways are networks of interactions

not all networks are pathwaysnot all networks are pathways

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

A network is a collection of interactionsA network is a collection of interactions

Pathways are a subset of networksPathways are a subset of networksAll pathways are networks of interactions, however not All pathways are networks of interactions, however not

all networks are pathways!all networks are pathways!

Pathway is a biological network that corresponds to Pathway is a biological network that corresponds to a specific physiological process or phenotypea specific physiological process or phenotype

Biological pathways

Biological components interacting with each other Biological components interacting with each other over time to bring about a single biological effectover time to bring about a single biological effect

Pathways can be broken down sub-pathways Pathways can be broken down sub-pathways

Some common pathways: Some common pathways: signal transductionsignal transductionmetabolic pathways, gene regulatory pathwaysmetabolic pathways, gene regulatory pathways

Entities in one pathway can be found in othersEntities in one pathway can be found in others

3 types of interactions that can be mapped into pathways 3 types of interactions that can be mapped into pathways

protein (enzyme) – metabolite (ligand)protein (enzyme) – metabolite (ligand) metabolic pathwaysmetabolic pathways

protein – proteinprotein – proteincell signaling pathways, protein complexescell signaling pathways, protein complexes

protein – geneprotein – genegenetic networksgenetic networks

KEGG KEGG http://www.genome.jp/kegg/http://www.genome.jp/kegg/BioCyc BioCyc http://www.biocyc.org/http://www.biocyc.org/Reactome http://www.reactome.org/Reactome http://www.reactome.org/GenMAPP http://www.genmapp.org/GenMAPP http://www.genmapp.org/BioCarta http://www.biocarta.com/BioCarta http://www.biocarta.com/TransPATH http://www.biobase-TransPATH http://www.biobase-

international.com/pages/index.php?international.com/pages/index.php?id=transpathdatabasesid=transpathdatabases

Pathguide Pathguide – the pathway resource list – the pathway resource list http://www.pathguide.org/http://www.pathguide.org/

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 Analysishttp://www.ingenuity.com/products/pathways_analysis.html

PathwayStudiohttp://www.ariadnegenomics.com/products/pathway-studio/

PathwayArchitect http://www.selectscience.net

Cytoscapehttp://www.cytoscape.org/

Biological Networkshttp://biologicalnetworks.net/

GeneGOhttp://www.genego.com/

Nanduri etal (unpublished)

GO term enrichment

Nanduri etal (unpublished)

Nanduri etal (unpublished)

Nanduri etal (unpublished)

Nanduri etal (unpublished)