Description

This column shows the expression of genes in specific tissues using the Affymetrix U74b chip. Together with the GNF U74a and GNF U74c columns, this displays the Mouse Gene Expression Atlas 1 from the Genomics Institute of the Novartis Research Foundation (GNF). Currently, the full spectrum of tissues is available only on the U74a chip.

By default, the column shows the ratio of expression of a gene in a specific set of tissues to the expression of the gene overall. A gene that is more highly expressed in a tissue is colored red, and a less expressed gene is shown in green. The values are colored on a logarithmic scale. This coloring is standard, but is the opposite of what an inexperienced user might expect: in this case, red means go and green means stop! Black indicates that a gene is neither over- nor under-expressed in the tissue. Uncolored boxes (white on most browsers) represent missing data.

Column Configuration

• Absolute expression values: The display can be configured to show absolute expression values rather than ratio values. To toggle the display, select the absolute option from the values pulldown menu. Absolute expression values are shown in shades of gray, with higher expression levels shown in lighter shades. As with ratio values, absolute values are colored on a logarithmic scale.
• Color scheme: Color-blind users can switch the coloring scheme from red/green to yellow/blue via the Expression ratio colors pulldown menu at the top of the Configuration page.
• Level of tissue detail: The tissue pulldown menu controls the amount and type of tissue data displayed. By default, only the median values for selected tissues are shown. To display the value of all individual experimental replicates of all tissues, select the all replicates option. To view a single median value for each tissue, choose the median of replicates option.
• Brightness: To increase or decrease the brightness of the expression colors, edit the number in the column's brightness text box. Values greater than 1.0 increase the brightness, while those less than 1.0 dim the color.

Methods

For detailed information about the experiments, see Su et al., "Large-scale analysis of the human and mouse transcriptomes.", PNAS, Mar 19, 2002.

When calculating expression ratios, the overall expression level in the denominator was calculated by first taking the median of replicates for each non-cancerous tissue, and then taking the median of these medians.

Credits