Multi-omics Pathway Visualization

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Different omics platforms—genomics, transcriptomics, proteomics, metabolomics and fluxomics—are generating new insights into how biological systems work at a molecular level. Although each individual …

Different omics platforms—genomics, transcriptomics, proteomics, metabolomics and fluxomics—are generating new insights into how biological systems work at a molecular level. Although each individual omics approach provides a global view of a specific cellular process, this view is limited to only one aspect. In order to gain a comprehensive understanding of the system as a whole, researchers are faced with the challenge of merging these different types of results.

PathVisio is an open source tool for drawing and editing biological pathways and visualizing and analyzing data. In order to make multi omics data visualization more intuitive we developed new add ons for the software to enable visualization of multiple data sets that can be about data of different types. This also allows visualization of data on the lines that symbolize interactions and reactions in the pathways, essentially adding edge visualization for network biology. In this way we can for instance show results of fluxomics studies or from dynamic system biology models.

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  • aptly characterizes one of the main goals of visualization, namely making it possible to absorb large amounts of data quickly.

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  • 1. Multi-omics Pathway VisualizationIntegration of interaction and flux data in PathVisio Anwesha Dutta BiGCaT - Maastricht UniversityBio-IT World Europe Conference & Expo 2012, 11 October, ViennaMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 1
  • 2. From Data to Visualization Data enriched Experimentation and Pathway Pathway data collection Genes Proteins Metabolites InteractionsMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 2
  • 3. What are Pathways?Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 3
  • 4. Pathway Representation Metabolites Proteins Nodes Transcripts miRNAs SNPs ... Flux values Edges Confidence scores ...Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 4
  • 5. Pathway Databases >300 pathway resourcesMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 5
  • 6. Wikipathways www.wikipathways.org • Wiki for biological pathways • Free and open source resource • Kegg & Reactome pathways also available Share, curate & discuss!Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo C, Pico AR. (2011) WikiPathways: building research communities onbiological pathways. NAR doi: 10.1093/nar/gkr1074 Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 6
  • 7. What is Data?Quantitative information about the different elements of apathway, obtained experimentally or by modeling.Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 7
  • 8. Why visualize Data? A picture is worth a thousand words ~Fred Barnard Visual representations of experimental results ease understanding.Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 8
  • 9. PathVisio www.pathvisio.orgPresenting and exploring biological pathways with PathVisio. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, ConklinBR, Evelo C. BMC Bioinformatics 2008, 9:399 (25 Sep 2008)Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 9
  • 10. Drawing biological pathwaysMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 10
  • 11. Download pathways WikipathwaysMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 11
  • 12. Data File Format• PathVisio accepts delimited text files• Prepare and export from ExcelMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 12
  • 13. Download annotation databases www.pathvisio.org/PathVisioDownloadA database for mapping interaction identifiersis in development and coming soon!Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 13
  • 14. Database identifier mapping Your data BridgeDB A pathway HMDB HMDB00122 HMDB00122 Kegg Compound HMDB01401 C00092 PubChem HMDB00124 69507Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 14
  • 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/BridgeDbCreator The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. van Iersel MP, PicoAR, Kelder T, Gao J, Ho I, Hanspers K, Conklin BR, Evelo CT. BMC Bioinformatics. 2010 Jan 4;11(1):5.Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 15
  • 16. Data mappedMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 16
  • 17. Data Visualized Legend: Metabolites visualized 0 5 with a color gradient Positive fluxes Negative fluxes Thickness of the arrows correspond to the amount of flux Example case :Flux & metabolite data visualized togetherMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 17
  • 18. Export Pathway• Export to image formats PNGMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 18
  • 19. Incorporation into workflows PathVisio PathVisioRPCMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 19
  • 20. PathVisio pointers• Completely free and open source• Fully compatible with Wikipathways• Modular architecture, easily extendable• Easy incorporation into pipelines• Very active mailing listMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 20
  • 21. Acknowledgements General Bioinformatics, Reading,UK Gladstone Institutes, SF, USA Max Planck Instt., TNO, Zeist, NL Berlin,Germany Funding Maastricht University, NL and many contributors around theMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 21
  • 22. Thank you for your time and attention! http://www.pathvisio.com/ wiki/PathVisioTutorials wikipathways-discuss@googlegroups.com anwesha.dutta@maastrichtuniversity.nlMulti-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 22