BIOINFORMATICS
DR. VÍCTOR TREVIÑO
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BT4007
Interactions
Pathways
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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)
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. Organismspecific 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
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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
"Reaction" Pathway
"REFERENCE" Pathway
"All organisms"
Pathway
"KO"
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
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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
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
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EBI PATHWAYS - REACTOME
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EBI PATHWAYS - REACTOME
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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

WikiPathways 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 TOOLS
• Pathways Explorer
(https://pathwayexplorer.genome.tugraz.at/)
• Cytoscape
(http://www.cytoscape.org)
• PathVisio
(http://www.pathvisio.org)
Main tool for analysing Networks
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GENETIC "PATHWAYS"

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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
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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