Bioinformatics Dr. Víctor Treviño vtrevino@itesm.mx BT4007 Interactions Pathways 1

Pathways Databases Pathway is "A sequence of biochemical compounds, and the reactions linking them, that describe a process in metabolism or catabolism" (Wikidictionary)

Pathways Databases – Wikipedia (Didactic) (link)

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 – 5/6 Types of Pathways

KEGG Pathways - Sizes Simple pathways Large pathways

KEGG - Sizes Complex Pathways

KEGG Pathways - Information "Links"

KEGG Pathways - Information … …

KEGG Pathways – Species, KO "Reaction" Pathway "REFERENCE" Pathway Specific in a Specie "KO" Pathway "All organisms" Pathway

KEGG Pathways - Genetic

KEGG Pathways - Environmental MAPK (TGFb) (others)

KEGG Pathways – Cellular Processes Focal Adhesion Chemotaxis etc

KEGG Pathways - Cancer

KEGG Pathways - Compounds

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 BioModels A 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. http://www.ebi.ac.uk/Databases/pathways.html

EBI Pathways - REACTOME

EBI Pathways - REACTOME Searches Overview

EBI Pathways - BioModels Few but precise models

EBI Pathways - BioModels

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. LINKS http://www.biocarta.com/

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 Pathways Explorer (https://pathwayexplorer.genome.tugraz.at/) Cytoscape (http://www.cytoscape.org) PathVisio (http://www.pathvisio.org) Main tool for analysing Networks

Genetic "Pathways" BIOBASE REGULONDB …

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/)

Interactions – New Experiments

Interactions – New Experiments

Interactions – New Experiments

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