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Importing KEGG pathway and mapping custom node graphics on Cytoscape

Importing KEGG pathway and mapping custom node graphics on Cytoscape. Kozo Nishida Keiichiro Ono Cytoscape retreat 2010 University of Michigan Jul 18, 2010. Outline. KEGG data import VizMap on the imported pathway Annotation import from TogoWS Future plans. Outline. KEGG data import

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Importing KEGG pathway and mapping custom node graphics on Cytoscape

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  1. Importing KEGG pathway and mapping custom node graphics on Cytoscape Kozo Nishida Keiichiro Ono Cytoscape retreat 2010 University of Michigan Jul 18, 2010

  2. Outline • KEGG data import • VizMap on the imported pathway • Annotation import from TogoWS • Future plans

  3. Outline • KEGG data import • VizMap on the imported pathway • Annotation import from TogoWS • Future plans

  4. KEGG • many other functions available • genes • ligand • ortholog (KO) • module • drug, disease global metabolism map (Okuda, Yamada, Nucleic Acids Res. 2008)

  5. KGML(KEGG Markup Language)and the reader • a xml format of KEGG graph objects • contains • diagram component (compound, enzyme) coordinate • reaction directionality old biopax imported result Glycolysis / Gluconeogenesis pathway imported by KGMLreader

  6. Global metabolism map in KEGG website (Okuda, Yamada, Nucleic Acids Res. 2008)

  7. Global metabolism map in Cytoscape

  8. Global metabolism map (Ecoli)

  9. Global metabolism map (Yeast)

  10. Global metabolism map (human)

  11. Outline • KEGG data import • VizMap on the imported pathway • Annotation import from TogoWS • Future plans

  12. VizMap example on global metabolism map(time-series1) Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed

  13. VizMap example on global metabolism map(time-series2) Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed

  14. VizMap example on global metabolism map(time-series3) Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed

  15. VizMap example on global metabolism map(time-series4) Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed

  16. VizMap example on global metabolism map(time-series5) Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed

  17. VizMap example on global metabolism map(time-series6) Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed

  18. Custom Node Graphics • new feature in 2.8 • using Google Chart Tools red line = expression profile(MT) blue line= expression profile(WT) orange background = over-expressed in MT than WT(Pval < 0.05) for KEGG module blue background = under-expressed.... Lysine biosynthesis

  19. Outline • KEGG data import • VizMap on the imported pathway • Annotation import from TogoWS • Future plans

  20. Information not included in KGML • in KGML • entry_id • short_name • not in KGML • id link to other database • Pathway • GO • UMBBD • KO • COG • Compound • PubChem • ChEBI • other KEGG metadata

  21. What is TogoWS ? • One-stop service for major biological databases (Katayama, Nakao, Nucleic Acids Res. 2010)

  22. TogoWS REST service http://togows.dbcls.jp/entry/database/ entry_id[,entry_id2,...]/field • http://togows.dbcls.jp/entry/pathway/bsu00010/dblinks • http://togows.dbcls.jp/entry/pathway/bsu00010/diseases • http://togows.dbcls.jp/entry/pathway/bsu00010/modules

  23. Outline • KEGG data import • VizMap on the imported pathway • Annotation import from TogoWS • Future plans

  24. Maplink node navigation usingNested Network Format (NNF) merge using maplink node One global differentially expressed pathway

  25. Custom pathway search user interface • search and selection input box specialized for  the KEGG attribute • highlight or show only the nodes or edges ( and the visual style) • filtering items • pathway category • KEGG module

  26. Floating information window for a pathway • pathway's expression diversity compared with other pathway expression diversity • pathway's centrality diversity compared with other pathway centralities

  27. Side-by-side comparison using different Visual Styles • visualize same pathway • but apply different organism, Visual Style, time-point etc. to compare

  28. Other future plans • data integration using other API • bridgedb • MASSBANK • extension using Processing visualizer • multi layered network • 3D visualization • animation • cooperation with other plugins • Webservice client plugin • CyAnimator • Advance network merge  • CentiScaPe

  29. Acknowledgement • Toshiaki Katayama (KGML, TogoWS) • Mitsuteru Nakao (TogoWS) • Biohackathon people • Google summer of code

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