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BIOINFORMATICS DR. VÍCTOR TREVIÑO [email protected] BT4007 Interactions Pathways

Bioinformatics Dr. Víctor Treviño [email protected] BT 4007

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Interactions Pathways. Bioinformatics Dr. Víctor Treviño [email protected] BT 4007. Pathway is "A sequence of biochemical compounds, and the reactions linking them, that describe a process in metabolism or catabolism" (Wikidictionary). Pathways Databases. (link). (link). - PowerPoint PPT Presentation

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Page 1: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

BIOINFORMATICSDR. VÍCTOR TREVIÑ[email protected]

InteractionsPathways

Page 2: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

[email protected]

PATHWAYS DATABASES Pathway is "A sequence of biochemical

compounds, and the reactions linking them, that describe a process in metabolism or catabolism" (Wikidictionary)

Page 3: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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PATHWAYS DATABASES – WIKIPEDIA (DIDACTIC)

(link) (link)

Page 4: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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

Page 5: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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.

Page 6: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG – 5/6 TYPES OF PATHWAYS

Page 7: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS - SIZES Simple pathways

Large pathways

Page 8: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG - SIZES Complex Pathways

Page 9: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS - INFORMATION

"Links"

Page 10: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS - INFORMATION

Page 11: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS – SPECIES, KO

"REFERENCE" Pathway "Reaction" Pathway

"KO"Pathway

"All organisms"Pathway

Specific in a Specie

Page 12: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS - GENETIC

Page 13: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS - ENVIRONMENTAL

MAPK

(TGFb)(others)

Page 14: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS – CELLULAR PROCESSES Focal Adhesion

Chemotaxis

etc

Page 15: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS - CANCER

Page 16: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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KEGG PATHWAYS - COMPOUNDS

Page 17: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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

Page 18: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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.

Page 19: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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EBI PATHWAYS - REACTOME

Page 20: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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EBI PATHWAYS - REACTOME Searches Overview

Page 21: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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EBI PATHWAYS - BIOMODELS Few but

precise models

Page 22: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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EBI PATHWAYS - BIOMODELS

Page 23: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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

Page 24: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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

Page 25: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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

http://www.pantherdb.org/

Page 26: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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PATHWAYS - TOOLS Pathways Explorer

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

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

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

Page 27: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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)

Page 28: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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GENETIC "PATHWAYS" BIOBASE REGULONDB …

Page 29: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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BIND Major database for protein interactions

Sold to Thomson, free accounts

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

Page 30: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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PATHWAYS + NETWORKS : HUBS Interactions, Pathways, Networks:

Bioinformatics Links Directory ( > 90 resources)

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

Page 31: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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INTERACTIONS – NEW EXPERIMENTS

Page 32: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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INTERACTIONS – NEW EXPERIMENTS

Page 33: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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INTERACTIONS – NEW EXPERIMENTS

Page 34: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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

Page 35: Bioinformatics Dr.  Víctor  Treviño vtrevino@itesm.mx BT 4007

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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