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Pathway Analysis Tools

Pathway Analysis Tools. Kristina Hettne Safety Assessment AstraZeneca R&D Mölndal, Sweden. Outline. Pathway analysis Tools Non-simulation Simulation Databases Summary. What do we mean by pathway analysis?. Different needs:

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Pathway Analysis Tools

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  1. Pathway Analysis Tools Kristina Hettne Safety Assessment AstraZeneca R&D Mölndal, Sweden

  2. Outline • Pathway analysis • Tools • Non-simulation • Simulation • Databases • Summary

  3. What do we mean by pathway analysis? • Different needs: • Find number of existing pathways for a specific compound (graphical representation of pathways) • Generate possible pathways for a specific compound (network generation) • Investigating the nature of the interactions, e.g. inhibition, transcription regulation, binding, etc. • Mathematical simulation of the interactions

  4. Pathway analysis tools • Divided into:

  5. Non-simulation tools • PathwayAssist • PathArt • KeyMolnet • Ingenuity Pathways Analysis • MetaCore

  6. PathwayAssist • Provider: Ariadne Genomics • Features: • Pathway editor • Natural Language Processing (NLP) derived database • Runs under Windows ME, 2000 and XP • Advantages: • Import data from protein-protein interaction databases (BIND, DIP) and metabolic databases (KEGG) • Application Programming Interface (API) • Disadvantages: • Not manually curated • URL: • http://www.ariadnegenomics.com/products/pathway.html

  7. PathArt • Provider: Jubilant Biosys • Features: • Pathway editor • Manually curated database • Runs under Windows NT, 2000, XP, and Linux and Solaris platforms • Advantages: • Many pathways • Disadvantages: • Visualisation is less advanced compared to other applications, though possibility exist to use Spotfire and PathwayAssist for better visualisation • URL: • http://www.jubilantbiosys.com/pd.htm

  8. KeyMolnet • Provider: Institute of Medicinal Medical Design • Features: • Pathway editor • Manually curated database • Network generator • Runs under Windows 2000 and XP • Advantages: • No special advantages compared to other products • Disadvantages: • Many important features are still under development (can not add own pathways) • URL: • http://www.immd.co.jp/page3_1e.html

  9. Ingenuity Pathways Analysis • Provider: Ingenuity • Features: • Pathway editor • Manually curated database • Network generator • Runs under Windows 98, NT and 2000 • Advantages: • Nice way of illustrating cellular context • Disadvantages: • Small number of reference pathways, relies much on network generation • URL: • http://www.ingenuity.com/products/pathways_analysis.html

  10. MetaCore • Provider: GeneGo • Features: • Pathway editor • Manually curated database • Network generator • Runs under Windows • Advantages: • No special advantages compared to other products • Disadvantages: • No special disadvantages compared to other products • URL: • http://www.genego.com/about/products.shtml

  11. Simulation tools • PathwayLab (InNetics, http://innetics.com/) • aMaze (Service de Conformation de Macromolécules Biologiques et de Bioinformatique, Université libre de Bruxelles, http://balabio.dcs.gla.ac.uk/drg/path_analysis/) • Metabolic Pathway Editor (Enzymes and Metabolic Pathways database Project, http://mpe.empproject.com/) • Virtual Cell (The National Resource for Cell Analysis and Modeling, http://www.nrcam.uchc.edu/) • Visual Cell (Gene Network Sciences, http://www.gnsbiotech.com/science.php) • GeneCesus (Yale Gerstein Lab, http://bioinfo.mbb.yale.edu/genome/) • Patika (Center for Bioinformatics at Bilkent University, http://www.patika.org/) • Systems Biology Workbench (Systems Biology Workbench Development Group at California Institute of Technology, http://sbw.sourceforge.net/) • BioUML (Biosoft.Ru, http://www.biouml.org/) • Cellware (Systems Biology Group at the Bioinformatics Institute, Singapore, http://www.bii.a-star.edu.sg/research/sbg/cellware/index.asp)

  12. Pathway Databases • 32 different databases • Different approaches • Flat-file with non-interactive images (many) • Relational (commercial solutions) • XML format (few) • Concealed format • Different topics (metabolic, signaling, etc.)

  13. Grouping of the databases • General • Metabolic • Signaling • Gene expression • Protein-protein interaction • Specific

  14. Pathway Databases: Overview

  15. CSNDB (Cell Signaling Networks Database)

  16. BioCarta

  17. KEGG (Kyoto Encyclopedia of Genes and Genomes)

  18. Summary • Different kind of pathway analysis questions need to be answered • Different applications answer different questions, no single tool exist that answer all questions • Most public database sources are very specific • Pathways are usually presented as non-interactive images

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