Copyright OpenHelix. No use or reproduction without express written consent1
ArrayExpress A resource for functional genomics data and analysis Materials prepared by: Agnes J. Radek, Ph.D. Jennifer M. Williams, Ph.D. Updated: Q Version 5
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:
Copyright OpenHelix. No use or reproduction without express written consent4 ArrayExpress Homepage Old AE Interface
Copyright OpenHelix. No use or reproduction without express written consent5 High Quality Data Collection Standards - FGED Types of Records: Protocol P-XXXX-n Experiment E-XXXX-n Array A-XXXX-n
Copyright OpenHelix. No use or reproduction without express written consent6 Credit to the ArrayExpress Developers Citation Reference
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
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:
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
Copyright OpenHelix. No use or reproduction without express written consent10 TFF3 Gene Expression Report Expression Profiles Experimental Factors Gene Summary
Copyright OpenHelix. No use or reproduction without express written consent11 Gene Report - Top Functional Ontology Terms Various IDs and other gene info Synonyms & Orthologs
Copyright OpenHelix. No use or reproduction without express written consent12 Gene Report – Experimental Factors Experimental Factors Heatmap of expression change Expression image
Copyright OpenHelix. No use or reproduction without express written consent13 Gene Report – Expression Profiles Expression Profile Report in Atlas Experiment Report from ArrayExpress Archive
Copyright OpenHelix. No use or reproduction without express written consent14 Expression Profile Report in Atlas Publication link Toggle graph display Expression Scores
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:
Copyright OpenHelix. No use or reproduction without express written consent16 Gene Expression Atlas Homepage Example: “down in” human, condition = muscular dystrophy
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
Copyright OpenHelix. No use or reproduction without express written consent18 Advanced Search Modification Add GO term = muscle development
Copyright OpenHelix. No use or reproduction without express written consent19 Modified Advanced Search Results Atlas Advanced Searches = Powerful Expression Analyses
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:
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
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
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
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
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 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
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
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
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:
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
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
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
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
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
Copyright OpenHelix. No use or reproduction without express written consent34 Data Retrieval – Raw Data Exp. factor values Scan names Click to download raw data
Copyright OpenHelix. No use or reproduction without express written consent35 Exported Data Progress bar Download data matrix AnnotationSignalDetection Upload to Expression Profiler es/2.3/bioc/html/ArrayExpress. html
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
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
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:
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
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
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
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:
Copyright OpenHelix. No use or reproduction without express written consent43