1. Human Genetics Unit Managing The High-Throughput Gene Expression Dataflow in Eurexpress Lalit Kumar Yin Chen Duncan Davidson Richard Baldock

2. Human Genetics Unit The Need 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) 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 2

3. Human Genetics Unit 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 3 The Response 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

4. Human Genetics Unit 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 4 Some Statistics 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

5. Human Genetics Unit Eurexpress Data 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 5

6. Human Genetics Unit 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 6 Data Flow

7. Human Genetics Unit 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 7 Data Flow ------------------ - --- - - - ---- - - - - - - ----------------- - ----- - ---- - - - - - - -------- - -- - ----- -------------- - Section images + Experiment info in XML form Annotators use FIATAS ------------------ - --- - - - ---- - - - - - - ----------------- - ----- - ---- - - - - - - -------- - -- - ----- -------------- - Annotations in XML Form DB Server + Web server Users get data via Eurexpress.org Template data Assay DATAPRCESSINGDATAPRCESSING +

8. Human Genetics Unit 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 8 FIATAS 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 web- server via a web-service web-service integrates annotation data into the system

9. Human Genetics Unit 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 9 www.eurexpress.org

10. Human Genetics Unit Assay View 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 10

11. Human Genetics Unit Browse Access 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 11

12. Human Genetics Unit Query Access 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 12

13. Human Genetics Unit 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 13 Analysis & APIs Similarity Matching Clustering Functional Analysis geneDAS BioMART

14. Human Genetics Unit 14/06/2016 Lalit Kumar (MRC HGU) @ UK e-Science All Hands Meeting 2008 14 Thank You! Any questions? Contact: Richard.Baldock@hgu.mrc.ac.uk Lalit.Kumar@hgu.mrc.ac.uk