interactions pathways. [email protected] pathway is "a sequence of biochemical compounds, and...
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PATHWAYS DATABASES
Pathway is "A sequence of biochemical compounds, and the reactions linking them, that describe a process in metabolism or catabolism" (Wikidictionary)
KEGG First (and main)
source of Biochemical Pathways
SOURCE of important information in functional genomics
Also contain other useful information
http://www.genome.jp/kegg
KEGG - OVERVIEW
The KEGG PATHWAY database is a collection of graphical diagrams (KEGG pathway maps) representing molecular interaction networks in various cellular processes. Each reference pathway is manually drawn and updated. Organism-specific pathways (green-colored pathways) are computationally generated based on the KO assignment in individual genomes.
KEGG PATHWAYS – SPECIES, KO
"REFERENCE" Pathway "Reaction" Pathway
"KO"Pathway
"All organisms"Pathway
Specific in a Specie
KEGG PATHWAYS
Rich information about biochemical, genetic, cellular, environmental, cancer and compounds pathways
IMPORTANT!!! Source of SET OF GENES (compounds) for functional genomics experiments
EBI - PATHWAYS
http://www.ebi.ac.uk/Databases/pathways.html
Database Description
BioModelsA database of annotated biological models that allows biologists to store, search and retrieve published mathematical models of biological interests.
Reactome
A curated database of biological processes in humans. Reactome will not only be useful to general biologists as an online textbook of biology, but also to bioinformaticians for making new discoveries about biological pathways.
BIOCARTA PATHWAYS
Observe how genes interact in dynamic graphical models. Our online maps depict molecular relationships from areas of active research. In an "open source" approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species. Find both classical pathways as well as current suggestions for new pathways.
http://www.biocarta.com/
LINKS
WIKIPATHWAYS
WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community
http://www.wikipathways.org
PANTHER PATHWAYS
Primarly signalling pathways CellDesigner (for designing pathways) SMBL language
http://www.pantherdb.org/
PATHWAYS - TOOLS
Pathways Explorer(https://pathwayexplorer.genome.tugraz.at/)
Cytoscape(http://www.cytoscape.org)
PathVisio(http://www.pathvisio.org)
PATHWAYS TOOLS
Main tool for analysing Networks• Pathways Explorer(https://pathwayexplorer.genome.tugraz.at/)
• Cytoscape(http://www.cytoscape.org)
• PathVisio(http://www.pathvisio.org)
BIND
Major database for protein interactions
Sold to Thomson, free accounts
http://bond.unleashedinformatics.com/Action?
PATHWAYS + NETWORKS : HUBS
Interactions, Pathways, Networks: Bioinformatics Links Directory ( > 90 resources)
PathGuide (http://www.pathguide.org/)
INTERACTION DATABASES QUERY
("Database Management Systems"[MAJR] OR "Databases, Nucleic Acid"[MAJR] OR "Databases, Protein"[MAJR] OR "Databases, Genetic"[MAJR] OR "Databases, Factual"[MAJR] OR "Databases, Bibliographic"[MAJR]) AND (bind OR interaction) AND database[TI]
169 Results
ACTIVITY Take a gene (your favourite) Search for pathways containing the gene Use a couple of pathways Select a compound/product from each pathway to "estimate"
what would you do to accelerate and slow-down the pathway Top 2 interacting genes
Report results of each step Justify your selections Use at least two pathways databases Use at least two other databases to extract other information Pathways chosen should contain at least 10 genes, 10
compunds Send results to googlegroups Compare results of your collegues