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 VizMap on the imported pathway Annotation import from TogoWS Future plans

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

a xml format of KEGG graph objects contains o diagram component (compound, enzyme) coordinate o reaction directionality Glycolysis / Gluconeogenesis pathway imported by KGMLreader old biopax imported result 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 module blue 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 database o 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 entry_id[,entry_id2,...]/field

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

Maplink node navigation using Nested 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 items o pathway category o 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 visualize same pathway but apply different organism, Visual Style, time-point etc. to compare

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

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