Description
This column shows the expression of genes in various phases
of the fly life cycle. The experiments were replicated two times each.
By default, the column shows the ratio of gene expression at a specific
life cycle phase to expression of the gene in mixed egg-to-adult
cultures. A gene that is more highly expressed in a life cycle phase 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 life
cycle phase. 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 expression detail: The phases pulldown menu
controls the amount of life cycle data displayed. By default, only the
median values for selected life cycle phases are shown. To display the value of
all individual experimental replicates of all phases,
select the all replicates option. To view a single median value for each
phase, 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
The data in this column were collected as described in the paper
Arbeitman MN, et al. (2002).
"Gene expression during the life cycle of Drosophila melanogaster".
Science 2002 Sep 27;297(5590):2270-5.
We retrieved the data from the
Stanford Microarray
Database.
To associate particular genes with expression data we use a fairly simple-minded
scheme. First we align the cDNA sequences around which the probes were designed to
the genome. Then for each gene we pick the cDNA sequence with the alignment that most
overlaps the gene as the source for expression data for that gene. Since many of the cDNA
sequences and probes designed for the cDNA sequences just cover part of the gene, in most
cases different splice varients of a gene will end up mapped to the same cDNA sequence.
Credits
Many thanks to
Arbeitman et al. for making the data available.