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Alvis Brazma, Array Express Gene Expression Atlas, fged_seattle_2013

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From microarrays to RNA-seq. From archiving experiments to Gene Expression Atlas.

From microarrays to RNA-seq. From archiving experiments to Gene Expression Atlas.

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  • 1. From microarrays to RNAseq From archiving experiments to Gene Expression Atlas Alvis Brazma European Bioinformatics Institute
  • 2. European Bioinformatics Institute (EBI) •  EBI is in Hinxton, ~10 miles South of Cambridge, UK Wellcome Trust Genome Campus •  EBI is part of EMBL, ~like CERN for molecular biology •  ~500 scientific and IT staff at EBI •  Hosting the ELIXIR node (details to follow)
  • 3. Building an archive of public gene expression data (www.ebi.ac.uk/arrayexpress)
  • 4. Building an archive of public gene expression data (www.ebi.ac.uk/arrayexpress)
  • 5. Search for cancer
  • 6. 150 citations of ArrayExpress publications using the data in 2011:
  • 7. From microarrays to RNAseq ArrayExpress9
  • 8. NGS vs Array data in ArrayExpress 1 10 100 1000 10000 2009 2010 2011 2012 Array data Sequencing data
  • 9. Experiment details
  • 10. MINSEQE - Minimum Information about a high-throughput SeQuencing Experiment 1.  The description of the biological system and the particular states that are studied 2.  The sequence read data for each assay 3.  The 'final' processed (or summary) data for the set of assays in the study 4.  The experiment design including sample data relationships 5.  General information about the experiment 6.  Essential experimental and data processing protocols
  • 11. ArrayExpress ArrayExpress Archive Primary DB Expression Atlas Added Value DB Curation EFO annotation statistical computationsSubmissions and GEO import curation Users – bioinformaticians Users – all biologists
  • 12. Query for genes Query for conditions Mission - making ArrayExpress data accessible to every biologist Igfbp4
  • 13. Experiment view
  • 14. Baseline Expression e.g. which genes are expressed in a normal human kidney? Differential Expression e.g. which genes are up- regulated in pancreatic islets of pregnant mice? www-test.ebi.ac.uk/gxa
  • 15. www-test.ebi.ac.uk/gxa Baseline Expression quality control pain%ng  by  shardcore  (h2p://www.shardcore.org/)   low-quality reads NNACGANNNNN mapping Baseline   quantification summarization RNA-seq Processing Pipeline
  • 16. www-test.ebi.ac.uk/gxa Baseline Expression Experimental Factors: •  Tissue •  RNA type •  Cellular component •  Cell lineExperiments so far (RNA-seq): •  Illumina Body Map (16 runs) •  Transcriptome of DBAxC57BL/6J mice (36 runs) •  RNA-seq of long coding and long non coding RNAs from ENCODE cell lines (162 runs) •  RNA-seq of 6 tissues from 10 species to investigate the evolution of gene expression levels in mammalian organs (127 runs)
  • 17. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  • 18. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  • 19. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  • 20. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  • 21. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  • 22. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  • 23. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues) *Rando, T. A. Nature 441, 1080-1086 (29 June 2006) | doi:10.1038/nature04958 Stem cells, ageing and the quest for immortality
  • 24. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  • 25. www-test.ebi.ac.uk/gxa Baseline Expression Future Plans – Inclusion of Proteomics Data
  • 26. www-test.ebi.ac.uk/gxa Baseline Expression Future Plans – Genome Browser View
  • 27. www-test.ebi.ac.uk/gxa Baseline Expression Future Plans – Comparable Experiments Now Future
  • 28. Future Plans – Atlas Home Page www-test.ebi.ac.uk/gxa We need your feedback!
  • 29. Robert Petryszak
  • 30. Funding •  EMBL member countries •  European Commission FP7 grants
  • 31. Questions www-test.ebi.ac.uk/gxa