Stemformatics.org was built for stem cell researchers with minimal experience in bioinformatics, providing a centralised portal with an intuitive, gene-centric search interface, transparent access to primary references, and high-quality graphics. It was developed from the recognition of the value of published gene expression signatures, and acknowledged the difficulty in identifying, searching, comparing or analysing this data in generic array repositories. All data has been curated, and includes quality metrics for each dataset and array platform. The workbench area provides a secure area to upload and analyse user-defined lists, and steps users through simple analysis workflows including differential expression , correlated gene lists and clustering. Statistical approaches use GenePattern as the analysis-engine, and a translation feature encourages and facilitates more sophisticated analyses on external analysis sites . Gene list annotations include predictions on protein domains, GO annotations, subcellular localization and pathway membership.
· biology-centric queries of public stem cell datasets
· workbench analysis area for comparison or correlation of samples/genes
· secure upload of proprietary gene lists with annotation features
· file 'translation' for easy upload into external gene expression analysis tools