0
From microarrays to RNAseq
From archiving experiments to Gene
Expression Atlas
Alvis Brazma
European Bioinformatics Instit...
European Bioinformatics Institute (EBI)
•  EBI is in Hinxton, ~10 miles South of Cambridge, UK
Wellcome Trust Genome Campu...
Building an archive of public gene expression
data (www.ebi.ac.uk/arrayexpress)
Building an archive of public gene expression
data (www.ebi.ac.uk/arrayexpress)
Search for cancer
150 citations of ArrayExpress publications
using the data in 2011:
From microarrays to RNAseq
ArrayExpress9
NGS vs Array data in ArrayExpress
1
10
100
1000
10000
2009 2010 2011 2012
Array data
Sequencing data
Experiment details
MINSEQE - Minimum Information about a
high-throughput SeQuencing Experiment
1.  The description of the biological system a...
ArrayExpress
ArrayExpress
Archive
Primary DB
Expression
Atlas
Added Value DB
Curation
EFO annotation
statistical computati...
Query for genes
Query for conditions
Mission - making ArrayExpress data
accessible to every biologist
Igfbp4
Experiment view
Baseline Expression
e.g. which genes are
expressed in a normal
human kidney?
Differential Expression
e.g. which genes are ...
www-test.ebi.ac.uk/gxa
Baseline Expression
quality control
pain%ng	
  by	
  shardcore	
  (h2p://www.shardcore.org/)	
  
lo...
www-test.ebi.ac.uk/gxa
Baseline Expression
Experimental Factors:
•  Tissue
•  RNA type
•  Cellular component
•  Cell lineE...
www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
*Rando, T. A. Nature 441, 1080-1086 (29 Ju...
www-test.ebi.ac.uk/gxa
Baseline Expression
Illumina Body Map (16 human tissues)
www-test.ebi.ac.uk/gxa
Baseline Expression
Future Plans – Inclusion of Proteomics Data
www-test.ebi.ac.uk/gxa
Baseline Expression
Future Plans – Genome Browser View
www-test.ebi.ac.uk/gxa
Baseline Expression
Future Plans – Comparable Experiments
Now Future
Future Plans – Atlas Home Page
www-test.ebi.ac.uk/gxa
We need your feedback!
Robert Petryszak
Funding
•  EMBL member countries
•  European Commission FP7 grants
Questions
www-test.ebi.ac.uk/gxa
Alvis Brazma, Array Express Gene Expression Atlas, fged_seattle_2013
Alvis Brazma, Array Express Gene Expression Atlas, fged_seattle_2013
Alvis Brazma, Array Express Gene Expression Atlas, fged_seattle_2013
Alvis Brazma, Array Express Gene Expression Atlas, fged_seattle_2013
Alvis Brazma, Array Express Gene Expression Atlas, fged_seattle_2013
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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.

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Transcript of "Alvis Brazma, Array Express Gene Expression Atlas, fged_seattle_2013"

  1. 1. From microarrays to RNAseq From archiving experiments to Gene Expression Atlas Alvis Brazma European Bioinformatics Institute
  2. 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. 3. Building an archive of public gene expression data (www.ebi.ac.uk/arrayexpress)
  4. 4. Building an archive of public gene expression data (www.ebi.ac.uk/arrayexpress)
  5. 5. Search for cancer
  6. 6. 150 citations of ArrayExpress publications using the data in 2011:
  7. 7. From microarrays to RNAseq ArrayExpress9
  8. 8. NGS vs Array data in ArrayExpress 1 10 100 1000 10000 2009 2010 2011 2012 Array data Sequencing data
  9. 9. Experiment details
  10. 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. 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. 12. Query for genes Query for conditions Mission - making ArrayExpress data accessible to every biologist Igfbp4
  13. 13. Experiment view
  14. 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. 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. 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. 17. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  18. 18. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  19. 19. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  20. 20. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  21. 21. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  22. 22. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  23. 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. 24. www-test.ebi.ac.uk/gxa Baseline Expression Illumina Body Map (16 human tissues)
  25. 25. www-test.ebi.ac.uk/gxa Baseline Expression Future Plans – Inclusion of Proteomics Data
  26. 26. www-test.ebi.ac.uk/gxa Baseline Expression Future Plans – Genome Browser View
  27. 27. www-test.ebi.ac.uk/gxa Baseline Expression Future Plans – Comparable Experiments Now Future
  28. 28. Future Plans – Atlas Home Page www-test.ebi.ac.uk/gxa We need your feedback!
  29. 29. Robert Petryszak
  30. 30. Funding •  EMBL member countries •  European Commission FP7 grants
  31. 31. Questions www-test.ebi.ac.uk/gxa
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