### 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.