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

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

3. Pathways Databases – Wikipedia (Didactic)
(link)

4. KEGG First (and main) source of Biochemical Pathways
SOURCE of important information in functional genomics
Also contain other useful information

5. 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.

6. KEGG – 5/6 Types of Pathways

7. KEGG Pathways - Sizes
Simple pathways
Large pathways

8. KEGG - Sizes
Complex Pathways

9. KEGG Pathways - Information
"Links"

10. KEGG Pathways - Information… …

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

12. KEGG Pathways - Genetic

13. KEGG Pathways - Environmental
MAPK
(TGFb)
(others)

14. KEGG Pathways – Cellular Processes
Focal Adhesion
Chemotaxis
etc

15. KEGG Pathways - Cancer

16. KEGG Pathways - Compounds

17. KEGG Pathways
Rich information about biochemical, genetic, cellular, environmental, cancer and compounds pathways
IMPORTANT!!! Source of SET OF GENES (compounds) for functional genomics experiments

18. 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.

19. EBI Pathways - REACTOME

20. EBI Pathways - REACTOME
Searches
Overview

21. EBI Pathways - BioModels
Few but precise models

22. EBI Pathways - BioModels

23. 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

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

25. Panther Pathways Primarly signalling pathways
CellDesigner (for designing pathways)
SMBL language

26. Pathways - Tools
Pathways Explorer (
Cytoscape (
PathVisio (

27. Pathways Tools
Pathways Explorer (
Cytoscape (
PathVisio (
Main tool for analysing Networks

28. Genetic "Pathways"
BIOBASE
REGULONDB …

29. BIND Major database for protein interactions
Sold to Thomson, free accounts

30. Pathways + Networks : Hubs
Interactions, Pathways, Networks: Bioinformatics Links Directory ( > 90 resources)
PathGuide (

31. Interactions – New Experiments

32. Interactions – New Experiments

33. Interactions – New Experiments

34. 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

35. 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