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Transcriptomics on Bio-Linux

Joe Wood. Transcriptomics on Bio-Linux. Transcriptomics on Bio-Linux. GeneSpring and GeNet Maxd MIAME EST pipeline. GeneSpring. Silicon Genetics Installed on Bio-Linux Licences available for EG grant holders GeNet Database MIAME compliant. GeneSpring Features. Data normalisation

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Transcriptomics on Bio-Linux

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  1. Joe Wood Transcriptomics on Bio-Linux

  2. Transcriptomics on Bio-Linux • GeneSpring and GeNet • Maxd • MIAME • EST pipeline

  3. GeneSpring • Silicon Genetics • Installed on Bio-Linux • Licences available for EG grant holders • GeNet Database • MIAME compliant

  4. GeneSpring Features • Data normalisation • Data clustering • 3D visualisation • Pathway views • Expression profile comparison • Scripting • Advanced statistical tools

  5. Data Normalisation

  6. Data clustering

  7. 3D Visualisation

  8. Expression Profile Comparison

  9. Pathway Views

  10. Advanced Statistical Tools

  11. Scripting

  12. GeNet Data Repository • Central database hosted by EGTDC • Store and share microarray data • GeNet Public Data Repository • ~6500 MIAME annotated microarray experiments • Upload to GeneSpring as example data sets

  13. MIAME • MIAME – minimum information about a microarray experiment • Standard for recording microarray experiments • Required by major journals inc. Nature and Lancet • MIAME/Env

  14. MIAME and GeneSpring • Controlled by standardattributes.xml • Defines which attributes for a particular sample must be entered • Required, recommended, optional • Set MIAME options to required – MIAME compliance

  15. Maxd • Microarray Group, University of Manchester • http://www.bioinf.man.ac.uk/microarray/maxd • Open Source • Installed on Bio-Linux

  16. Maxd at EGTDC URL: http://envgen.nox.ac.uk/maxd.html • Maxd homepage • Maxd course notes • Extra installation instructions

  17. Maxd components • MaxdMaker • MaxdLoad • MaxdView

  18. MaxdMaker • Maxd dataschema • EBI -Array Express (MIAME) • maxd.sql • MySQL • PostgreSQL • Oracle

  19. MaxdMaker

  20. Array scanner text file Maxd database MaxdLoad

  21. Array scanner text file Maxd database MaxdView

  22. Why maxd? • Open source • MIAME compliant • Complement to GeneSpring • Extra analysis methods

  23. EST Pipeline • Bio-Linux EST pipeline in development • Trace files • EST sequences • Clustered • Annotated • Submit to dbEST

  24. Integrating GeneSpring/EST • GeneSpring 'genomes' • GeneSpider automatically annotates • GeneTable files • Can create own GeneTables • EST annotations, other lab-specific annotations

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