Multi-omics Pathway Visualization
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The document presents multi-omics pathway visualization integration, focusing on how interaction and flux data can be represented effectively. It highlights various tools and resources like PathVisio and WikiPathways for visualizing biological pathways, along with the importance of data visualization in bioinformatics. Additionally, it discusses data mapping services through BridgeDb to facilitate the integration of various biological identifier systems.
Multi-omics Pathway Visualization
- 1. Multi-omics Pathway Visualization Integration of interaction and flux data in PathVisio Anwesha Dutta BiGCaT - Maastricht University Bio-IT World Europe Conference & Expo 2012, 11 October, Vienna Multi-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 Interactions Multi-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 resources Multi-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 on biological 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 a pathway, 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.org Presenting and exploring biological pathways with PathVisio. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, 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 pathways Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 10
- 11. Download pathways Wikipathways Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 11
- 12. Data File Format • PathVisio accepts delimited text files • Prepare and export from Excel Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 12
- 13. Download annotation databases www.pathvisio.org/PathVisioDownload A database for mapping interaction identifiers is 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 69507 Multi-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 identifier Create 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, Pico AR, 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 mapped Multi-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 together Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 17
- 18. Export Pathway • Export to image formats PNG Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 18
- 19. Incorporation into workflows PathVisio PathVisioRPC Multi-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 list Multi-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 the Multi-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.nl Multi-omics Pathway Visualization Bio-IT World Europe Conference & Expo 2012 22
Editor's Notes
- #9: aptly characterizes one of the main goals of visualization, namely making it possible to absorb large amounts of data quickly.