1. Copyright OpenHelix. No use or reproduction without express written consent1

2. ArrayExpress A resource for functional genomics data and analysis Materials prepared by: Agnes J. Radek, Ph.D. Jennifer M. Williams, Ph.D. www.openhelix.com Updated: Q4 2010 Version 5

3. Copyright OpenHelix. No use or reproduction without express written consent3 ArrayExpress Agenda Introduction and Credits Basic Atlas Search & Display Advanced Atlas Searches Archive Search Old AE Search Interface Summary Exercises ArrayExpress: http://www.ebi.ac.uk/arrayexpress/

4. Copyright OpenHelix. No use or reproduction without express written consent4 ArrayExpress Homepage Old AE Interface

5. Copyright OpenHelix. No use or reproduction without express written consent5 High Quality Data Collection Standards - FGED http://www.mged.org/index.html Types of Records: Protocol P-XXXX-n Experiment E-XXXX-n Array A-XXXX-n

6. Copyright OpenHelix. No use or reproduction without express written consent6 Credit to the ArrayExpress Developers Citation Reference

7. Copyright OpenHelix. No use or reproduction without express written consent7 An Enormous Amount of High Quality Data! Access to submitted data sets Analysis of Gene Expression ArrayExpress – a powerful resource

8. Copyright OpenHelix. No use or reproduction without express written consent8 ArrayExpress Agenda Introduction and Credits Basic Atlas Search & Display Advanced Atlas Searches Archive Search Old AE Search Interface Summary Exercises ArrayExpress: http://www.ebi.ac.uk/arrayexpress/

9. Copyright OpenHelix. No use or reproduction without express written consent9 Gene Expression Atlas - Basic Search Gene Name 1.Enter gene name or attribute (GO term etc.) Example=TFF 2.Select direction (up, down or either) Example = either 3.Enter condition (disease, tissue, etc.) Example = blank 4.Select species Example = Homo sapiens 5.Click “Query” button TFF

10. Copyright OpenHelix. No use or reproduction without express written consent10 TFF3 Gene Expression Report Expression Profiles Experimental Factors Gene Summary

11. Copyright OpenHelix. No use or reproduction without express written consent11 Gene Report - Top Functional Ontology Terms Various IDs and other gene info Synonyms & Orthologs

12. Copyright OpenHelix. No use or reproduction without express written consent12 Gene Report – Experimental Factors Experimental Factors Heatmap of expression change Expression image

13. Copyright OpenHelix. No use or reproduction without express written consent13 Gene Report – Expression Profiles Expression Profile Report in Atlas Experiment Report from ArrayExpress Archive

14. Copyright OpenHelix. No use or reproduction without express written consent14 Expression Profile Report in Atlas Publication link Toggle graph display Expression Scores

15. Copyright OpenHelix. No use or reproduction without express written consent15 ArrayExpress Agenda Introduction and Credits Basic Atlas Search & Display Advanced Atlas Searches Archive Search Old AE Search Interface Summary Exercises ArrayExpress: http://www.ebi.ac.uk/arrayexpress/

16. Copyright OpenHelix. No use or reproduction without express written consent16 Gene Expression Atlas Homepage http://www.ebi.ac.uk/gxa/ Example: “down in” human, condition = muscular dystrophy

17. Copyright OpenHelix. No use or reproduction without express written consent17 Search Results Rows = Genes Click to Gene Report Number of experiments, click for more details Columns = Conditions

18. Copyright OpenHelix. No use or reproduction without express written consent18 Advanced Search Modification Add GO term = muscle development

19. Copyright OpenHelix. No use or reproduction without express written consent19 Modified Advanced Search Results Atlas Advanced Searches = Powerful Expression Analyses

20. Copyright OpenHelix. No use or reproduction without express written consent20 ArrayExpress Agenda Introduction and Credits Basic Atlas Search & Display Advanced Atlas Searches Archive Search Old AE Search Interface Summary Exercises ArrayExpress: http://www.ebi.ac.uk/arrayexpress/

21. Copyright OpenHelix. No use or reproduction without express written consent21 ArrayExpress Archive Use the Experiments Archive to: find COMPLETE STUDIES by a common parameter (e.g. organism, author, biological phenomenon) find datasets supporting publications retrieve data submit data Gateway to Archive Find experiments Help with query Submitter / reviewer data access point Data content

22. Copyright OpenHelix. No use or reproduction without express written consent22 ArrayExpress Archive – Basic Search Example 1 Enter keyword → set filters (optional) Fields searched: Experiment title Experiment description Sample and exp. factor attributes Species Publication title Experiment and array accession numbers E-TABM-132 Search term Query Number of experiments & assays

23. Copyright OpenHelix. No use or reproduction without express written consent23 ArrayExpress Archive – Basic Search Example 2 Basic search: a combination of free-text search and filtering Browse → set filters → add keyword (optional) Browse experiments Help Filters Adjust # of exps. per page morphogenesis Query Species List of ALL archived experiments Technology types

24. Copyright OpenHelix. No use or reproduction without express written consent24 Archive Search Results Accession number Number of hybs. Species Date of entry Link to processed data Link to raw data Link to AE Atlas Title Number of experiments & hybs. Save as text Click to expand experiment Search criteria Print Export to ExcelExport as RSS feed

25. Copyright OpenHelix. No use or reproduction without express written consent25 Experiment Report – Expanded View Detailed description of study by submitter MIAME score Citation, links to PubMed & journal Experiment types Experimental factors Sample attributes http://www.ebi.ac.uk/microarray/doc/help/browse_results.html Results help Links to: AE Atlas, array record, protocols, AE Advanced Interface Downloadable files: data, description, sample – data relationship table, graphic view of exp. design, array design

26. Copyright OpenHelix. No use or reproduction without express written consent26 Experiment – Sample and Data Relationship Sample and Data Relationship Table Additional file formats Sample → Processing → Data

27. Copyright OpenHelix. No use or reproduction without express written consent27 Experiment Design Image BioSource = D.rerio BioSample = Tissue LabeledExtract Hyb. Link to data Boxes can be clicked for further info, links to protocols Experiment title BioSample = Extract

28. Copyright OpenHelix. No use or reproduction without express written consent28 ArrayExpress Agenda Introduction and Credits Basic Atlas Search & Display Advanced Atlas Searches Archive Search Old AE Search Interface Summary Exercises ArrayExpress: http://www.ebi.ac.uk/arrayexpress/

29. Copyright OpenHelix. No use or reproduction without express written consent29 ArrayExpress Archive – Old Interface To Old Archive Search Interface Search for experiments Search for arrays Search for protocols http://www.ebi.ac.uk/microarray-as/aer/entry

30. Copyright OpenHelix. No use or reproduction without express written consent30 Search for Experiments – Many Options E-XXXX-n A-XXXX-n keyword(s) Search by array accession #, name, or provider Query with field-specific terms Array Species Experiment type Experimental factors Description keyword Author Laboratory Publication Species Exp. type Exp. factor Journal OR E-MEXP-171 Search description field by keyword(s) Search by experiment accession number

31. Copyright OpenHelix. No use or reproduction without express written consent31 Search for Experiments - Result Search criteria Number of matches Accession number Exp. design type Links to downloadables & additional info Data retrieval Description

32. Copyright OpenHelix. No use or reproduction without express written consent32 Data Retrieval – Processed Data, Part 1 Step 1. Select experimental conditions Number of available data groups Exp. factor values Select all Invert selections X X X X X X

33. Copyright OpenHelix. No use or reproduction without express written consent33 Data Retrieval – Processed Data, Part 2 Step 2. Select quantitation types Step 3. Select annotation types Step 4. Export data Links to software & protocols Select quantitation types X X Link to array record Select annotation types X Export data

34. Copyright OpenHelix. No use or reproduction without express written consent34 Data Retrieval – Raw Data Exp. factor values Scan names Click to download raw data

35. Copyright OpenHelix. No use or reproduction without express written consent35 Exported Data Progress bar Download data matrix AnnotationSignalDetection Upload to Expression Profiler www.bioconductor.org/packag es/2.3/bioc/html/ArrayExpress. html

36. Copyright OpenHelix. No use or reproduction without express written consent36 Querying for Arrays Search by array accession number Rat Agilent (Part of) array name Array provider Number of matches Search criteria Accession number Array name (by provider) Version Provider Descriptions Download array design spreadsheet Find all experiments with this Array

37. Copyright OpenHelix. No use or reproduction without express written consent37 Querying for Protocols Search by protocol accession number OR By protocol type Protocol: treatment of biomaterial (e.g. growth, genetic modification, extraction) treatment of an array (e.g.hybridization, imaging) treatment of data (e.g. normalization) Description Accession number Protocol type Title

38. Copyright OpenHelix. No use or reproduction without express written consent38 ArrayExpress Agenda Introduction and Credits Basic Atlas Search & Display Advanced Atlas Searches Archive Search Old AE Search Interface Summary Exercises ArrayExpress: http://www.ebi.ac.uk/arrayexpress/

39. Copyright OpenHelix. No use or reproduction without express written consent39 Summary Query full Archive of user-submitted data Query annotated subset of data across genes, conditions and experiments

40. Copyright OpenHelix. No use or reproduction without express written consent40 Detailed Results Detailed Gene Reports Detailed Experiment Reports Query results across multiple genes & conditions Search Results include detailed information

41. Copyright OpenHelix. No use or reproduction without express written consent41 Powerful Search Interfaces Basic & Advanced Atlas Searches Filtered Archive Searches Direct Archive Searches with Old AE Interface You choose the interface that best suits your needs

42. Copyright OpenHelix. No use or reproduction without express written consent42 ArrayExpress Agenda Introduction and Credits Basic Atlas Search & Display Advanced Atlas Searches Archive Search Old AE Search Interface Summary Exercises ArrayExpress: http://www.ebi.ac.uk/arrayexpress/

43. Copyright OpenHelix. No use or reproduction without express written consent43