projects.bigcat.unimaas.nl/pathvisiorpc

Anwesha Bohler1,3, Martina Kutmon1,3, Martijn P. van Iersel4, Thomas Kelder5, Kristina Hanspers2, Alexander R. Pico2, Chris T. Evelo1,3

1: Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands, 2: Gladstone Institute of Cardiovascular Disease, San Francisco,

California, USA, 3: Netherlands Consortium for Systems Biology (NCSB), The Netherlands, 4: General Bioinformatics, Reading, UK, 5: TNO, Zeist, The Netherlands.

Add references (pathway = bibliography) Annotate genes, proteins,

metabolites ...

Annotate interactions

Share on

Free & open

source

• Wiki style pathway database.

• Reactome pathways also available

• Fully compatible with PathVisio

• +23 species (Human, Mouse, ...)

drawn in 2

• Extensions of the core application • Provide specialized task−specific features • Available through the new plugin repository • One click installation through plugin manager

• Pathway Editor and Analysis Tool • Completely free and open source • Fully compatible with Wikipathways • Modular architecture, easily extendable with Plugins • Easy incorporation into pipelines using the XML-RPC interface

PathVisioRPC

www.pathvisio.org

www.wikipathways.org

www.pathvisio.org/plugins/plugins-repo

Central metabolism of E. coli

Export as images

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* Thicker the arrow more the flux * Negative fluxes indicate that the reaction proceeds in the opposite direction

Hypergeometric Test

Higher zscore = greater significance!

Over representation analysis of GO terms

GO Elite Plugin Work in progress

PathVisioRPC

Produce this image directly from R

Positive fluxes Negative fluxes

Legend

Simultaneously visualize Transcriptomics, Proteomics , Metabolomics and fluxomics data Visualize Time series data Here, we visualize time series metabolite concentration data alongwith in vivo carbon fluxes

XML-RPC interface of PathVisio

java –jar PathVisioRPC.jar “7777” #Start server library("XMLRPC") #Load library server = http://localhost:7777 #Set server address xml.rpc(server, "PathVisio.visualizeData", filepath_pathway, filepath_pgex, folderpath_databases, folderpath_results)

Create pathways, visualize data, perform pathway statistics in your favourite analytical environment Add PathVisio easily to your data analysis pipeline

Pathways ranked by enrichent

score

Graph with ES (Enrichment Score) and list of the core enrichments

Pathways ranked by z-score

GSEA Plugin Work in progress

Edge Visualization Plugin Work in progress

anwesha.dutta@maastrichtuniversity.nl National Institutes of Health (GM080223, HG003053), BioRange 1.2.4 research program of Netherlands Bioinformatics Centre,

Transnational University Limburg, Agilent Thought Leader grant of Chris Evelo, and Netherlands Consortium for Systems Biology.

Thanks for the funding Contact :

Reactome

REACT_112439

Rhea

35711

Visualize Data

Gene Set Enrichment Analysis Gene Ontology Analysis