Path visio3

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Path visio3

  1. 1. PathVisio 3 NBIC Conference 2013 1
  2. 2. PathVisio www.pathvisio.orgPathVisio 3 NBIC Conference 2013 2
  3. 3. New Structure Refactored using the OSGi framework for a better, modular system that can be easily extended with plugins. Plugins • Extensions of the core application that provide features relevant for a specific task. • This allows users to build an application with all the necessary modules relevant for their work. • Plugins are available through the new plugin repository and they can be installed through the plugin manager from within the application.PathVisio 3 NBIC Conference 2013 3
  4. 4. Plugin repository & managerThe new plugin manager displays available plugins in therepository to the users and provides easy and fast installation.PathVisio 3 NBIC Conference 2013 4
  5. 5. Core Software + Plugins PATHVISIO WORKFLOWPathVisio 3 NBIC Conference 2013 5
  6. 6. • Create Pathways / Get Pathways• Visualize Data• Perform pathway analysis• Export ResultsPathVisio 3 NBIC Conference 2013 6
  7. 7. But unlike any other drawing program, usingas you would in any other In PathVisio you can draw pathways, PathVisio you can annotateyour genes, proteins, program, like PowerPoint orusing database identifiers. drawing metabolites and interactions Photoshop.PathVisio 3 NBIC Conference 2013 7
  8. 8. Drawing with standards SBGN Plugin MIM Plugin http://www.sbgn.org/http://discover.nci.nih.gov/mim/ Luna A.et al, PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs), Bioinformatics Applications Note, doi:10.1093/bioinformatics/btr336 PathVisio 3 NBIC Conference 2013 8
  9. 9. Pathway ValidatorThis plugin ensures the correct usage of the MIM notation in pathway diagrams. Chandan K. et al, PathVisio-Validator: a rule-based validation plugin for graphical pathway notations, Bioinformatics Applications Note, doi:10.1093/bioinformatics/btr694 PathVisio 3 NBIC Conference 2013 9
  10. 10. www.wikipathways.orgWikipathways Share, curate & discuss! • Wiki for biological pathways • Free and open source resource • Reactome pathways also available • Fully compatible with PathVisioPathVisio 3 NBIC Conference 2013 10
  11. 11. Download pathwaysPathVisio 3 NBIC Conference 2013 11
  12. 12. Standard Workflow using PathVisio• Create Pathways / Get Pathways• Visualize Data• Perform pathway analysis• Export ResultsPathVisio 3 NBIC Conference 2013 12
  13. 13. Data Import http://www.pathvisio.org/wiki/DatabasesMappsData : quantitative information about the different elements of The system code is used to identify whicha pathway, obtained experimentally or by modeling database a particular identifier belongs to.PathVisio accepts delimited text filesPathVisio 3 NBIC Conference 2013 13
  14. 14. Database identifier mapping BridgeDB HMDB HMDB00122 HMDB00122 Kegg HMDB01401 Compound C00092 HMDB00124 ?? PubChem 69507 Data annotated with HMDB IDs Pathway metabolites annotated with different IDsPathVisio 3 NBIC Conference 2013 14
  15. 15. BridgeDb www.bridgedb.org • Id mapping framework for bioinformatics applications • Translates identifiers from one system to another • Links out to online information for an identifierCreate your own BridgeDb derby database!http://www.bridgedb.org/wiki/BridgeDbCreatorPathVisio 3 NBIC Conference 2013 15
  16. 16. Gene Databasehttp://www.pathvisio.org/downloads/download-bridgedbs/• 32 species supported• Annotation database for metabolites• Annotation database for interactions (in development)PathVisio 3 NBIC Conference 2013 16
  17. 17. Data mappedPathVisio 3 NBIC Conference 2013 17
  18. 18. PathVisio core application includes the visualization plugin tovisualize data on datanodes(genes, proteins, metabolites).The EdgeVisualization plugin in PathVisio enables visualizingdata on the reactions and interactions of the pathways.PathVisio 3 NBIC Conference 2013 18
  19. 19. Data Visualized Legend: Metabolites visualized 0 5 with a color gradient Positive fluxes Negative fluxes Thickness of the arrows correspond to the amount of fluxExample case :Flux & metabolite data visualized together This gives a global view of flux distribution over the entire biological pathwayPathVisio 3 NBIC Conference 2013 19
  20. 20. Standard Workflow using PathVisio• Create Pathways / Get Pathways• Visualize Data• Perform pathway analysis• Export ResultsPathVisio 3 NBIC Conference 2013 20
  21. 21. Over Representation AnalysisThe Z-score can be used as a measure for howmuch a subset of genes is different from the rest R (rn ) zscore = N R R n1 n(1 )( 1 ) N N N1• r = changed genes in Pathway• n = total genes in Pathway• R = changed genes• N = total genes Other enrichment calculation methods Ackermann M et al., A general modular framework for gene set enrichment analysis, BMC bioinformatics, 2009 PathVisio 3 NBIC Conference 2013 21
  22. 22. Z-score CalculationPathVisio 3 NBIC Conference 2013 22
  23. 23. Gene Ontology Plugin Create Gene Ontology (GO) pathways in PathVisio 1. Browse GO Tree 2. Create GO pathwayPathVisio 3 NBIC Conference 2013 23
  24. 24. Gene Set Enrichment Analysis pluginPathVisio 3 NBIC Conference 2013 24
  25. 25. Plugin for categorizing pathways based on GO terms(in development) Notch signalling pathway http://wikipathways.org/index.php/Pathway:WP268PathVisio 3 NBIC Conference 2013 25
  26. 26. Standard Workflow using PathVisio• Create Pathways / Get Pathways• Visualize Data• Perform pathway analysis• Export ResultsPathVisio 3 NBIC Conference 2013 26
  27. 27. Export pathway images and analysisresults• Export to image formats • Png PNG • Svg • Tiff• Export as pdf• Html Export Plugin : export pathway images, statistics results and backpages as html pages• Biopax3GPML : import biopax (.owl) files as GPML for use in PathVisio and export Wikipathways pathways as .owl files• GPML plugin : Cytoscape plugin which allows a pathway to be opened as a cytoscape networkPathVisio 3 NBIC Conference 2013 27
  28. 28. Incorporation into workflows PathVisioRPCPathVisio 3 NBIC Conference 2013 28
  29. 29. Summary• Completely free and open source• Fully compatible with Wikipathways• Modular architecture, easily extendable• Easy incorporation into pipelines• Very active mailing listPathVisio 3 NBIC Conference 2013 29
  30. 30. PathVisio 3 NBIC Conference 2013 30
  31. 31. Acknowledgements Max Planck Instt., TNO, Zeist, NL Gladstone Institutes, SF, USA Berlin,Germany Funding General Bioinformatics, Reading,UK Maastricht University, NL and many contributors around thePathVisio 3 NBIC Conference 2013 31
  32. 32. Thank you for your time and attention! wikipathways-discuss@googlegroups.com anwesha.dutta@maastrichtuniversity.nlPathVisio 3 NBIC Conference 2013 32

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