cytoscape retreat 2010_demo
DESCRIPTION
http://cytoscape.wodaklab.org/wiki/CytoscapeRetreat2010TRANSCRIPT
Importing KEGG pathway and mapping custom node graphics on Cytoscape
Kozo NishidaKeiichiro Ono
Cytoscape retreat 2010University of Michigan
Jul 18, 2010
Outline
• KEGG data import
• VizMap on the imported pathway
• Annotation import from TogoWS
• Future plans
Outline
• KEGG data import
• VizMap on the imported pathway
• Annotation import from TogoWS
• Future plans
KEGG
• many other functions availableo geneso ligando ortholog (KO)o moduleo drug, disease
global metabolism map(Okuda, Yamada, Nucleic Acids Res. 2008)
• a xml format of KEGG graph objects
• containso diagram component
(compound, enzyme) coordinate
o reaction directionality
Glycolysis / Gluconeogenesispathway imported by KGMLreader
old biopax importedresult
KGML(KEGG Markup Language)and the reader
Global metabolism map in KEGG website
(Okuda, Yamada, Nucleic Acids Res. 2008)
Global metabolism map in Cytoscape
Global metabolism map (Ecoli)
Global metabolism map (Yeast)
Global metabolism map (human)
Outline
• KEGG data import
• VizMap on the imported pathway
• Annotation import from TogoWS
• Future plans
VizMap example on global metabolism map(time-series1)
Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed
VizMap example on global metabolism map(time-series2)
Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed
VizMap example on global metabolism map(time-series3)
Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed
VizMap example on global metabolism map(time-series4)
Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed
VizMap example on global metabolism map(time-series5)
Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed
VizMap example on global metabolism map(time-series6)
Red = over-expressed in MT than WT (Pval < 0.05), Green = under-expressed
Custom Node Graphics
• new feature in 2.8• using Google Chart Tools
Lysine biosynthesis
red line = expression profile(MT)blue line= expression profile(WT)orange background = over-expressed in MT than WT(Pval < 0.05) for KEGG moduleblue background = under-expressed....
Outline
• KEGG data import
• VizMap on the imported pathway
• Annotation import from TogoWS
• Future plans
Information not included in KGML
not in KGML• id link to other
databaseo Pathway
GO UMBBD
o KO COG
o Compound PubChem ChEBI
• other KEGG metadata
in KGML• entry_id• short_name
What is TogoWS ?
• One-stop service for major biological databases
(Katayama, Nakao, Nucleic Acids Res. 2010)
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
Outline
• KEGG data import
• VizMap on the imported pathway
• Annotation import from TogoWS
• Future plans
Maplink node navigation usingNested Network Format (NNF)
merge using maplink node
One global differentially expressed pathway
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 itemso pathway categoryo KEGG module
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
Side-by-side comparison using different Visual Styles
• Compare (same) pathway with applying different organism, Visual Style, time-point etc.
Other future plans
• data integration using other APIo bridgedbo MASSBANK
• extension using Processing visualizero multi layered networko 3D visualizationo animation
• cooperation with other pluginso Webservice client plugino CyAnimatoro Advance network merge o CentiScaPe
Acknowledgement
• Toshiaki Katayama (KGML, TogoWS)
• Mitsuteru Nakao (TogoWS)
• Biohackathon people
• Google summer of code