Figure 1

A SPIEDw worked example. The SPIEDw web page screen shot showing the various controls in the left column. A gene expression profile is uploaded, the user chooses whether to perform an exhaustive search or search only an abridged dataset comprising the most regulated genes. The latter is the appropriate option for performing gene list enrichment queries. Searches can be restricted to specific species and the number of top scoring samples returned can be increased beyond the default 100. We have performed a full search of SPIEDw with a profile corresponding to EGFR blockage in mouse neural stem cells [15]. The results column at the left lists the series id and sample id together with the correlation score and significance. The 'magnifying glass’ button enables the user to see how the query scores against all the samples in the given series, displayed in the results column on the right. For example, the EGFR antagonism profile scores highly against a study of PI3K/AKT inhibition in mouse mammary carcinoma cells [16], and as expected, this correlation is positive with the inhibitor treated samples and negative with the control samples.