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Jano van Hemert Jano van Hemertwww.dgemap.org 3 years EU-funded design study Goal: design the organisational & collaborative structures,

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Presentation on theme: "Jano van Hemert Jano van Hemertwww.dgemap.org 3 years EU-funded design study Goal: design the organisational & collaborative structures,"— Presentation transcript:

1 Jano van Hemert

2 Jano van Hemertwww.dgemap.org 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

3 Jano van Hemertwww.dgemap.org Consortium National e-Science Centre MRC Human Genetics Unit University of Newcastle

4 Jano van Hemertwww.dgemap.org 4 work packages

5 Jano van Hemertwww.dgemap.org 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

6 Jano van Hemertwww.dgemap.org Laboratory process

7 Jano van Hemertwww.dgemap.org From 2D sections to 3D models

8 Jano van Hemertwww.dgemap.org Framework: Edinburgh Mouse Atlas Space and Anatomy

9 Jano van Hemertwww.dgemap.org Space and Anatomy anatomical name

10 Jano van Hemertwww.dgemap.org Gene Expression Database Query: by both space and text...

11 Jano van Hemertwww.dgemap.org emage: Query by space

12 Jano van Hemertwww.dgemap.org emage: Query by space

13 Jano van Hemertwww.dgemap.org Silicon processes Data mining Human-mouse link Other data sources (OMIM, GDX, …) Other data sources (OMIM, GDX, …) Visualisation

14 Jano van Hemertwww.dgemap.org The Developing Human e-Portal

15 Jano van Hemertwww.dgemap.org Web services exist

16 Jano van Hemertwww.dgemap.org 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

17 Jano van Hemertwww.dgemap.org Mouse-human interoperability

18 Jano van Hemertwww.dgemap.org ‘McMahon’ Data TS17 Hierarchical clustering

19 Jano van Hemertwww.dgemap.org Hierarchical clustering Myt1l Dlx5 ‘McMahon’ Data TS17

20 Jano van Hemertwww.dgemap.org Let biologists cluster data

21 Jano van Hemertwww.dgemap.org Clustering: viewing the output

22 Jano van Hemertwww.dgemap.org What are association rules? Based on a set of transactions We want to derive rules of the form X => 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)

23 Jano van Hemertwww.dgemap.org Association Rules In the context of gene expression: if Gene 1 and Gene 2 then Gene 3 where a transaction equals a set of genes expressing together at the same time in the same anatomical component Alternative: if Component 1 then Component 2 and Component 3 where a transaction equals a number of components expressing the same gene at the same time

24 Jano van Hemertwww.dgemap.org Association Rules Results Wnt1, Bmp4 => Shh Vcam1 => Kdr Emx2 => Otx Otx1, Pax6 => Otx Wnt1, Bmp4 => Shh Vcam1 => Kdr Emx2 => Otx Otx1, Pax6 => Otx Association rules with a minimum confidence of 90% Transaction: genes expressing in the same anatomical component in the same Theiler stage Source: the EMAGE database, using the editorial spatial annotations extracted on 2006/08/28 Techo-fact: extracted using web services called from a Perl script …

25 Jano van Hemertwww.dgemap.org Perl script

26 Jano van Hemertwww.dgemap.org 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?

27 Jano van Hemertwww.dgemap.org 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


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