Description
This column shows the expression of genes in specific tissues
using spotted microarrays manufactured at Stanford University.
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
Several column configuration options are available on the Configuration page,
which can be accessed via the configure button in the top menu.
-
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 Shyamsundar R
et al.
"A DNA microarray survey of gene expression in normal human tissues.",
Genome Biol. 2005 Feb 14;6(3):R22.
When calculating expression ratios, the overall expression level in the
denominator was calculated by first taking the median of replicates for
each tissue, and then taking the median of these medians.
Credits
The data for this column was kindly provided by the
Stanford Microarray Database.