Transcript The Eurexpress Project - All Hands Meeting 2011

Human Genetics Unit
Managing The High-Throughput
Gene Expression Dataflow in Eurexpress
Lalit Kumar
Yin Chen
Duncan Davidson
Richard Baldock
The Need
Human Genetics Unit
• In order to understand the developmental and
physiological roles of genes it is important to
know when and where genes are expressed
• EU’s 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
Human Genetics Unit
• 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
Human Genetics Unit
• 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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Human Genetics Unit
Data Flow
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Human Genetics Unit
Data Flow
Annotators use FIATAS
D
A
T
A
Section images
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------------------ --- - - - ---- - - - - - -- --- - - - -- - --------------------- ----- - ---- - - - - - -------- - -- - ------------------ -
Experiment info
in XML form
P
R
C
E
S
S
I
N
G
Assay
------------------ --- - - - ---- - - - - - -- --- - - - -- - --------------------- ----- - ---- - - - - - -------- - -- - ------------------ -
Users get data
via Eurexpress.org
Annotations in XML Form
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Template data
DB Server + Web server
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FIATAS
Human Genetics Unit
• 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 webserver 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
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Human Genetics Unit
Similarity Matching
Clustering
Functional Analysis
geneDAS
BioMART
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Human Genetics Unit
Thank You!
Any questions?
Contact:
[email protected]
[email protected]
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