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http://www.dgemap.org/ Jano van Hemert 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 Jano van Hemert www.dgemap.org Consortium National e-Science Centre MRC Human Genetics Unit University of Newcastle Jano van Hemert www.dgemap.org 4 work packages Jano van Hemert www.dgemap.org Three major goals 1. Facilitate collaboration over multiple laboratories 2. Improve ways for handling spatialtemporal data from gene expression studies 3. Provide integration with other technologies and databases to help biologists advance their studies Jano van Hemert www.dgemap.org Laboratory process Jano van Hemert www.dgemap.org From 2D sections to 3D models QuickTime™ and a YUV420 codec decompressor are needed to see this picture. Jano van Hemert www.dgemap.org Framework: Edinburgh Mouse Atlas Space and Anatomy QuickT ime™ and a YUV420 codec decompressor are needed t o see this picture. Jano van Hemert www.dgemap.org Space and Anatomy anatomical name Jano van Hemert www.dgemap.org Gene Expression Database • Query: by both space and text... Jano van Hemert www.dgemap.org emage: Query by space QuickTime™ and a Animation decompressor are needed to see this picture. Jano van Hemert www.dgemap.org emage: Query by space Jano van Hemert www.dgemap.org Silicon processes Data mining Human-mouse link Visualisation Jano van Hemert Other data sources (OMIM, GDX, …) www.dgemap.org The Developing Human e-Portal Jano van Hemert www.dgemap.org Web services exist Jano van Hemert www.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 Jano van Hemert www.dgemap.org Mouse-human interoperability Jano van Hemert www.dgemap.org Hierarchical clustering ‘McMahon’ Data TS17 Jano van Hemert www.dgemap.org Hierarchical clustering ‘McMahon’ Data TS17 Myt1l Dlx5 Jano van Hemert www.dgemap.org Let biologists cluster data Jano van Hemert www.dgemap.org Clustering: viewing the output Jano van Hemert www.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) Jano van Hemert www.dgemap.org 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 Jano van Hemert www.dgemap.org Association Rules Results Transaction: genes expressing in the same anatomical component in the same Theiler stage Wnt1, Bmp4 => Shh Vcam1 => Kdr Emx2 => Otx2 Otx1, Pax6 => Otx2 Techo-fact: extracted using web services called from a Perl script… Jano van Hemert Association rules with a minimum confidence of 90% 0.053 0.057 0.054 0.051 0.91 0.93 0.95 0.92 Source: the EMAGE database, using the editorial spatial annotations extracted on 2006/08/28 www.dgemap.org Perl script Jano van Hemert www.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? Jano van Hemert www.dgemap.org Thanks for your attention Susan Lindsay Demetrius Vouyiouklis Marie-Laure Muiras Xunxian Wang Mark Scott Alina Andras Jano van Hemert Malcolm Atkinson Jano van Hemert Yin Chen Richard Baldock Simon Woods Ken Taylor www.dgemap.org