Managing The HighThroughput Gene Expression Dataflow in Eurexpress

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Managing The High-ThroughputGene Expression
Dataflow in Eurexpress

• Lalit Kumar
• Yin Chen
• Duncan Davidson
• Richard Baldock

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The Need

• In order to understand the developmental and
  physiological roles of genes it is important to
  know when and where genes are expressed
• EUs FP6 framework defines Global in situ gene
  expression analysis in rodent models and human
  tissues as an area of research under the
  Thematic Priority 1 (Life Sciences and
  Biotechnology for Health)

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The Response

• Started in 2005, Eurexpress project aims to
  develop a transcriptome atlas for mouse embryo
• The atlas is to contain in situ gene expression
  data for 20,000 genes
• All expression patterns to be annotated with
  respect to a standard anatomy ontology
• The data to be delivered via web-browsers,
  standard web-services, advanced query interfaces
  and analysis tools

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Some Statistics

• Project will manage 450K (now 300K) cellular
  level resolution section images (when complete
  10TB data)
• To date images are grouped in 17K assays
• More than 13K of these assays have been
  annotated
• More than 500K annotation entries

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Eurexpress Data
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Data Flow
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Data Flow
Annotators use FIATAS
D A T A P R C E S S I N G
Section images

Assay
Users get data via Eurexpress.org
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Annotations in XML Form
Experiment info in XML form

Template data
DB Server Web server
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FIATAS

• Abbr. of Fast Image AnnoTAtion Software
• It can show section images in an assay at various
  resolution levels
• Annotators annotate the images against an
  ontology tree
• FIATAS sends the annotations data in XML format
  to HGU web-server via a web-service
• web-service integrates annotation data into the
  system

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www.eurexpress.org
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Assay View
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Browse Access
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Query Access
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Analysis APIs

• Similarity Matching
• Clustering
• Functional Analysis
• geneDAS
• BioMART

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Thank You!

• Any questions?

Contact Richard.Baldock_at_hgu.mrc.ac.uk Lalit.Kumar
_at_hgu.mrc.ac.uk