Array Express a Public Repository for Microarray Based

Array. Express - a Public Repository for Microarray Based Gene Expression Data European Bioinformatics Institute - EMBL outstation and German Cancer Research Centre

The decision to establish a public gene expression data repository for array based gene expression data F F F Responding to EBI Industry partner needs, EBI got involved in gene expression data analysis in 1997 As the result of this work the need for the repository became apparent about 18 months ago After consulting many of the major microarray laboratories world-wide, the decision was made to start designing the database (Nature 398, p. 646, March 99)

Array. Express database FA public repository for array based gene expression data F Draft conceptual design for a public repository for array based gene expression data in Rational Rose F In close collaboration with DKFZ and Sanger Centre F Discussions with other potential data submitters world wide

Expression Profiler F Internet based tool for gene expression data analysis tool (www. ebi. ac. uk/arrayexpress) with a database of yeast expression profiles for about 100 experimental conditions from Stanford and MIT F Option for uploading users own data F Available online (first online tool as far as we know) F Still under development, will be used as an “attractor” for data submissions

Motivation of the design F When representing data from physical experiments we have to decide on the level of pre-processing before storing F Two perspectives – – F One high level data analysis not loosing essential information number per spot vs. image, gene centric vs. spot centric

Conservative compromise F Raw data captured F Information structured in a way that high level views can be easily precomputed F Array. Express – – – image analysis output for each spot “divide and conquer” approach in annotations reusability of information already in the database

Two types of submissions F Experiment - a set of hybridisations F Array description

“Divide and conquer” approach F Experiment - a set of hybridisations F A single hybridisation - array + sample F Array description (grid + spots) – spots may be linked to genes F Sample description F Hybridisation analysis (scanning, quantitation, data)

Top level structure of Array. Express database Publication (e. g. , Pub. Med. Central) External links Array. Express Source (e. g. , Taxonomy) Target Experiment Hybridisation Analysis Array Gene (e. g. , EMBL)

Array. Express - the conceptual schema