1 / 26

Dr. Chris Evelo

Dr. Chris Evelo. What we do at: (also read the comments). PathVisio. www.pathvisio.org. Visualize data on biological pathways It can use gene expression, proteomics and metabolomics data Identify significantly changed processes.

cruz
Download Presentation

Dr. Chris Evelo

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Dr. Chris Evelo

  2. What we do at: (also read the comments)

  3. 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

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

  5. 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]

  6. Process the data…

  7. 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

  8. 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

  9. 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

  10. Can we show SNPs?

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

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

  13. Data integration

  14. 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

  15. “Bioinformatics to better understand biological data” wikipathways.org Data Integration arrayanalysis.org pathvisio.org

  16. Contact Details Dr. Chris Evelo chris.evelo@maastrichtuniversity.nl Department of Bioinformatics – BiGCaT Maastricht University PO Box 616 NL 6200 MD Maastrich The Netherlands T: +31-43-3881231 M: +31-646705001 Skype: chris_evelo Web: www.bigcat.unimaas.nl CV: http://unimaas.academia.edu/ChrisEvelo Publications: www.publicationslist.org/chris_evelo Twitter: www.twitter.com/chris_evelo

More Related