Bioinformatics Dr. Víctor Treviño vtrevino@itesm.mx BT 4007

BIOINFORMATICSDR. VÍCTOR TREVIÑOVTREVINO@ITESM.MXBT4007

InteractionsPathways

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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)

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PATHWAYS DATABASES – WIKIPEDIA (DIDACTIC)

(link) (link)

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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

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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.

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KEGG – 5/6 TYPES OF PATHWAYS

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KEGG PATHWAYS - SIZES Simple pathways

Large pathways

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KEGG - SIZES Complex Pathways

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KEGG PATHWAYS - INFORMATION

"Links"

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KEGG PATHWAYS - INFORMATION

…

…

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KEGG PATHWAYS – SPECIES, KO

"REFERENCE" Pathway "Reaction" Pathway

"KO"Pathway

"All organisms"Pathway

Specific in a Specie

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KEGG PATHWAYS - GENETIC

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KEGG PATHWAYS - ENVIRONMENTAL

MAPK

(TGFb)(others)

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KEGG PATHWAYS – CELLULAR PROCESSES Focal Adhesion

Chemotaxis

etc

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KEGG PATHWAYS - CANCER

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KEGG PATHWAYS - COMPOUNDS

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KEGG PATHWAYS Rich information about biochemical,

genetic, cellular, environmental, cancer and compounds pathways

IMPORTANT!!! Source of SET OF GENES (compounds) for functional genomics experiments

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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.

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EBI PATHWAYS - REACTOME

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EBI PATHWAYS - REACTOME Searches Overview

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EBI PATHWAYS - BIOMODELS Few but

precise models

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EBI PATHWAYS - BIOMODELS

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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

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WIKIPATHWAYS WikiPathway

s is an open, public platform dedicated to the curation of biological pathways by and for the scientific community

http://www.wikipathways.org

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PANTHER PATHWAYS Primarly signalling pathways CellDesigner (for designing pathways) SMBL language

http://www.pantherdb.org/

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PATHWAYS - TOOLS Pathways Explorer

(https://pathwayexplorer.genome.tugraz.at/)

Cytoscape(http://www.cytoscape.org)

PathVisio(http://www.pathvisio.org)

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PATHWAYS TOOLSMain tool for analysing Networks• Pathways Explorer

(https://pathwayexplorer.genome.tugraz.at/)

• Cytoscape(http://www.cytoscape.org)

• PathVisio(http://www.pathvisio.org)

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GENETIC "PATHWAYS" BIOBASE REGULONDB …

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BIND Major database for protein interactions

Sold to Thomson, free accounts

http://bond.unleashedinformatics.com/Action?

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PATHWAYS + NETWORKS : HUBS Interactions, Pathways, Networks:

Bioinformatics Links Directory ( > 90 resources)

PathGuide (http://www.pathguide.org/)

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INTERACTIONS – NEW EXPERIMENTS

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INTERACTIONS – NEW EXPERIMENTS

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INTERACTIONS – NEW EXPERIMENTS

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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

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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