Differential experiment page

Each differential experiment in Expression Atlas has its own Differential experiment page. On this page, differentially expressed genes (rows) in each comparison studied (columns) are displayed in a heatmap by colour intensity, according to the gradient bar above the heatmap (Figure 11). The heatmap ranks genes by absolute log2 fold-change. Blue cells indicate that the gene is down-regulated while red indicates up-regulated genes.

Mouse over a cell in the heatmap to see log2 fold-change and adjusted p-value (or t-statistic for microarray data) for differentially expressed gene in each comparison (Figure 11). Click on Select genome browser to view tracks to view gene expression results in the context of the genomic location of each gene (Figure 11). You can download the corresponding data using the buttons at the top right of the page (Figure 11).

The left section of the experiment page gives you the following options:

• Search for a particular gene
• Uncheck the ‘Most specific’ option to show genes that are differentially expressed genes in all comparisons first
• Select only up-regulated genes, only down-regulated genes or both
• Specify different criteria for differential expression (the default is log2 fold-change > 1 and adjusted p-value < 0.05). Only genes satisfying both criteria are displayed
• Select a subset of comparisons

The differential experiment page has an additional tab called Plots. This includes Enrichment analysis plots to see if any Gene Ontology, InterPro or Reactome terms are significantly over-represented in the set of differentially expressed genes. Just click on the title to display the plot (Figure 12).