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