modeling functional genomics datasets cvm8890-101 lessons 4&5 10 july 2007bindu nanduri
TRANSCRIPT
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.
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
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 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/