Baseline experiment page

Each baseline experiment in Expression Atlas has its own Baseline experiment page. If you want to see gene expression results for all genes in the experiment, you have to remove UMOD from the Genes box and click Apply (Figure 8A).

Figure 8 Baseline experiment page.

On a baseline experiment page, expression levels are displayed in a heatmap. The level of expression is relative to the colour intensity, as shown in the gradient bar above the heatmap (Figure 8F). Mouse over a cell in the heatmap to see expression values for each gene in each tissue (Figure 8I). Click on Select genome browser to view tracks to view gene expression results in the context of the genomic location of each gene (Figure 8G).

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

  • Search for a particular gene (Figure 8A)
  • Uncheck the ‘Most specific’ option to show genes with highest expression across all tissues first (Figure 8B)
  • Specify a different minimum expression level (the default is 0.5 TPMs) so that only genes expressed above this level are displayed (Figure 8C)
  • Switch units between TPM and FPKM (Figure 8D)
  • Select a subset of tissues under ‘Organism parts’ (Figure 8E)

When you search for a particular gene, e.g. IGLC2, you will be able to:

  1. Visualise variation among biological replicates (Figure 9A). Click on Switch to boxplot view to display a plot per tissue with the maximum, upper quartile, median, lower quartile and minimum expression values for each set of biological replicates.
  2. Explore co-expression (Figure 9B). Click on Add similarly expressed genes button below the heatmap to find genes with similar expression pattern.
Figure 9 Visualise variation among biological replicates and explore co-expression.