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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) 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 2 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 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 3 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 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 4 Eurexpress Data 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 Human Genetics Unit 5 Human Genetics Unit Data Flow 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 6 Human Genetics Unit Data Flow Annotators use FIATAS D A T A Section images + ------------------ --- - - - ---- - - - - - -- --- - - - -- - --------------------- ----- - ---- - - - - - -------- - -- - ------------------ - 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 + Template data DB Server + Web server 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 7 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 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 8 www.eurexpress.org 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 Human Genetics Unit 9 Assay View 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 Human Genetics Unit 10 Browse Access 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 Human Genetics Unit 11 Query Access 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 Human Genetics Unit 12 Analysis & APIs • • • • • 23/05/2017 Human Genetics Unit Similarity Matching Clustering Functional Analysis geneDAS BioMART Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 13 Human Genetics Unit Thank You! Any questions? Contact: [email protected] [email protected] 23/05/2017 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 14