Jano van Hemert

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http//www.dgemap.org/
Jano van Hemert
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3 years EU-funded design study

• Goal design the organisational collaborative
  structures, ethical framework, and molecular
  genetic informatics technologies necessary for
  a new research infrastructure which will
  accelerate an integrated European approach to
  gene expression in early human development

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Consortium
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4 work packages
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Three major goals

1. Facilitate collaboration over multiple
   laboratories
2. Improve ways for handling spatial-temporal data
   from gene expression studies
3. Provide integration with other technologies and
   databases to help biologists advance their studies

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Laboratory process
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From 2D sections to 3D models
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Framework Edinburgh Mouse Atlas
Space and Anatomy
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Space and Anatomy
anatomical name
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Gene Expression Database

• Query by both space and text...

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emage Query by space
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emage Query by space
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Silicon processes
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The Developing Human e-Portal
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Web services exist
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Where do workflows fit in?

• Advanced queries incorporating other DBs
• Linking genes with diseases (OMIM)
• Genetic pathways (Kegg)
• Mouse-human interoperability
• Using anatomical terms
• Using direct 3D to 3D model mapping
• Using spatial-temporal ontologies
• Data mining and processes
• Hierarchical Clustering
• Association rules

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Mouse-human interoperability
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Hierarchical clustering
McMahon Data TS17
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Hierarchical clustering
McMahon Data TS17
Myt1l
Dlx5
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Let biologists cluster data
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Clustering viewing the output
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What are association rules?

• Based on a set of transactions
• We want to derive rules of the form X gt Y
• Meaning, if X happens then Y happens
• X and
• X and Y are sets of items appearing in the
  transactions
• The rules come with numbers to express their
  quality with respect to the set of transactions
  (most common support and confidence)

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Association Rules

• In the context of gene expression if Gene1 and
  Gene2 then Gene3 where a transaction equals a set
  of genes expressing together at the same time in
  the same anatomical component
• Alternative if Component1 then Component2 and
  Component3 where a transaction equals a number of
  components expressing the same gene at the same
  time

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Association Rules Results
Transaction genes expressing in the same
anatomical component in the same Theiler stage
Association rules with a minimum confidence of
90
Wnt1, Bmp4 gt Shh 0.053 0.91 Vcam1 gt
Kdr 0.057 0.93 Emx2 gt Otx2 0.054 0.95 Otx1,
Pax6 gt Otx2 0.051 0.92
Techo-fact extracted using web services called
from a Perl script
Source the EMAGE database, using the editorial
spatial annotations extracted on 2006/08/28
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Perl script
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Main issues while using Taverna

• Need for more data mangling functions
• Need for more data formatting controls
• Pipelining and memory concerns
• Library of useful translations services
• Interaction Plug-in Architecture?
• What about Axis version 2?

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Thanks for your attention

• Susan Lindsay
• Demetrius Vouyiouklis
• Marie-Laure Muiras
• Xunxian Wang
• Mark Scott
• Alina Andras

Malcolm Atkinson Jano van Hemert Yin
Chen Richard Baldock Simon Woods Ken Taylor