1 / 27

Jano van Hemert

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

ace
Télécharger la présentation

Jano van Hemert

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. http://www.dgemap.org/ Jano van Hemert

  2. 3 years EU-funded design study Goal: design theorganisational & 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. National e-Science Centre MRC Human Genetics Unit University of Newcastle Consortium

  4. 4 work packages

  5. Three major goals • Facilitate collaboration over multiple laboratories • Improve ways for handling spatial-temporal data from gene expression studies • Provideintegrationwithother technologies and databases to help biologists advance their studies

  6. Laboratory process

  7. From 2D sections to 3D models

  8. Framework: Edinburgh Mouse Atlas Space and Anatomy

  9. Space and Anatomy anatomical name

  10. Gene Expression Database • Query: by both space and text...

  11. emage: Query by space

  12. emage: Query by space

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

  14. The Developing Human e-Portal

  15. Web services exist

  16. 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. Mouse-human interoperability

  18. Hierarchical clustering ‘McMahon’ Data TS17

  19. Hierarchical clustering ‘McMahon’ Data TS17 Myt1l Dlx5

  20. Let biologists cluster data

  21. Clustering: viewing the output

  22. 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. 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 Component3where a transaction equals a number of components expressing the same gene at the same time

  24. 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 => Shh 0.053 0.91 Vcam1 => Kdr 0.057 0.93 Emx2 => Otx2 0.054 0.95 Otx1, Pax6 => 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

  25. Perl script

  26. 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. 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

More Related