Tuesday, 16 June 2009

Gene Expression Atlas - 1.1 Released!


A major Atlas release happened yesterday, 1.1! Here's what's new:
  1. Ontology-driven interface
    is now used not only for query expansion, but actively in the user interface. You can choose terms from the ontology to construct your queries, your queries use the ontology to display hits and the ontology is used to organise the results display. A simple query for "brain" will produce a detailed listing of gene expression activity in all brain compartments, from cortex to hypothalamus, and will also give you a broad overview upwards through the semantic hierarchy to the central nervous system.
  2. List view of search results
    In addition to viewing search results as a heatmap, you can view them as an expandable list, viewing the condition/experiment hits for each gene in the result set. Here's a list view of transcriptional activity in zebrafish brain.
  3. Download results
    You can download your search results as tab-delimited files. The download link is at the top of every list view. This is an experimental feature - let us know how you find it. It's a bit on the slow side right now but we'll work on improving it if people find it useful.
  4. Experiment pages with gene plots and similarity search
    Each experiment has a page where a large, detailed gene expression plot can be viewed. You can plot multiple lines on the plot, selecting from top differentially expressed genes, genes similar to ones displayed, or any gene that matches your search criteria.

... and lots of small changes and bug fixes under the hood - improved index, some of the underlying mechanics and so on.

Additionally, we've graduated to a top-level EBI resource. We are now called Gene Expression Atlas, and the URL is http://www.ebi.ac.uk/gxa. All the old URLs will continue to work, but do update your bookmarks.

We are keen to hear your comments and requests - write to us here or email us at our mailing list (sign up on the Atlas homepage). There are lots of new and interesting things we are planning to roll out in the next several months!


--Misha Kapushesky and the Atlas team.