1 / 22

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:

urbain
Télécharger la présentation

Pathway Analysis Tools

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related