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Chris Evelo Department of Bioinformatics - BiGCaT Maastricht University The Netherlands

Where we are and where we are going Some slides showing developments at BiGCaT Read the comments as well to get a story. Chris Evelo Department of Bioinformatics - BiGCaT Maastricht University The Netherlands http://www.bigcat.unimaas.nl. Translational research. Target discovery

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Chris Evelo Department of Bioinformatics - BiGCaT Maastricht University The Netherlands

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  1. Where we are and where we are goingSome slides showing developments at BiGCaTRead the comments as well to get a story Chris Evelo Department of Bioinformatics - BiGCaT Maastricht University The Netherlands http://www.bigcat.unimaas.nl

  2. Translational research Target discovery Mechanisms 2 Infrastructure Biomarkers metabolic monitoring modeling imaging tissue collection

  3. Chronic disease metabolism chronic inflammation obesity

  4. PathVisio www.pathvisio.org • Visualize data on biological pathways • It can use gene expression, proteomics and metabolomics data • Identify significantly changed processes Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, Chris Evelo (2008) Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 9: 399

  5. Find the pathways:Biological processes in duodenal mucosa affected by glutamine administration

  6. adding data =adding colour ExamplePathVisio result Showing proteomics and transcriptomics results on the glycolysis pathway in mice liverafter starvation. [Data from Kaatje Lenaerts and MilkaSokolovic, analysis by Martijn van Iersel]

  7. Process the data…

  8. dbNP Architecture Simple Assay module Body weight, BMI, etc. GSCF Query module Templates Full-text querying Templates Templates Transcriptomics module Groups Subjects Raw data cell files Structured querying Result data p-values z-values Clean data gene expression Pathways, GO, metabolite profiles Events Protocols Profile-based analysis Epigenetics module Samples Assays Study comparison Raw data Nimblegen Illumina Resulting Genome Feature data Clean CPG islanddata Web user interface

  9. WikiPathways WikiPathways: Pathway Editing for the People. Alexander R. Pico, Thomas Kelder, Martijn P. van Iersel, Kristina Hanspers, Bruce R. Conklin, Chris Evelo. PLoS Biology2008: 6: 7. e184 Commentaries:Big data: Wikiomics. Mitch Waldrop. Nature 2008: 455, 22-25We the curators. Allison Doerr. Nature Methods 2008: 5, 754–755No rest for the bio-wikis. Ewen Callaway. Nature 2010: 468, 359-360 Public resource for biological pathways Anyone can contribute and curate More up-to-date representation of biological knowledge

  10. PPS1Liver Cytoscape visualization used to group Pathways with high z-score grouped together. Explains why there are relatively few significant genes, but many pathways with high z-score. All pathways

  11. Can we show SNPs?

  12. Problem: Identifier Mapping Entrez Gene 3643 ? Affymetrix probeset 100234_at

  13. BridgeDB: AbstractionLayer classIDMapperRdbrelational database interfaceIDMapper classIDMapperFiletab-delimitedtext classIDMapperBiomart web service

  14. Data integration

  15. Finally connect genetics to genomics using modelling Gene/Protein Y Metabolite X TF • Pathways can serve as model visualizations (NCSB) • MIM and SBNG integration with EBI. • Quantified SNP functions can be model input RS00005 RS00002 Gene/Protein Z RS00001 RS00003 RS00004 mi999 Metabolite Y

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