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

Interactions Pathways. Bioinformatics Dr. Víctor Treviño vtrevino@itesm.mx 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).

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

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  1. Interactions Pathways BioinformaticsDr. Víctor Treviñovtrevino@itesm.mxBT4007

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

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

  4. 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

  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. "Links" KEGG Pathways - Information

  10. KEGG Pathways - Information … …

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

  12. KEGG Pathways - Genetic

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

  14. Focal Adhesion Chemotaxis etc KEGG Pathways – Cellular Processes

  15. KEGG Pathways - Cancer

  16. KEGG Pathways - Compounds

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

  18. EBI - Pathways http://www.ebi.ac.uk/Databases/pathways.html

  19. EBI Pathways - REACTOME

  20. EBI Pathways - REACTOME • Searches • Overview

  21. EBI Pathways - BioModels • Few but precise models

  22. EBI Pathways - BioModels

  23. 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 pathwaysas well ascurrent suggestions for new pathways. BioCarta Pathways LINKS http://www.biocarta.com/

  24. WikiPathways • WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community http://www.wikipathways.org

  25. Primarly signalling pathways CellDesigner (for designing pathways) SMBL language Panther Pathways http://www.pantherdb.org/

  26. Pathways - Tools • Pathways Explorer(https://pathwayexplorer.genome.tugraz.at/) • Cytoscape(http://www.cytoscape.org) • PathVisio(http://www.pathvisio.org)

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

  28. Genetic "Pathways" • BIOBASE • REGULONDB • …

  29. Major database for protein interactions Sold to Thomson, free accounts BIND http://bond.unleashedinformatics.com/Action?

  30. Interactions, Pathways, Networks: Bioinformatics Links Directory ( > 90 resources) PathGuide (http://www.pathguide.org/) Pathways + Networks : Hubs

  31. Interactions – New Experiments

  32. Interactions – New Experiments

  33. Interactions – New Experiments

  34. ("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 Interaction Databases Query

  35. 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 Activity

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