anwesha bohler1,3, martina kutmon1,3, martijn p. …...projects.bigcat.unimaas.nl/pathvisiorpc...
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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
Publish!
* 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
[email protected] 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