Description

This column shows the expression of genes during the cell cycle of the budding yeast S. cerevisiae.

Cells from a synchronous yeast culture were collected at 17 time points taken at 10 minute intervals, covering nearly 2 full cell cycles. By default, the column shows the ratio of gene expression at a specific cell cycle phase to expression of the gene overall. A gene that is more highly expressed in a cell 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 cell cycle phase. 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 cell cycle detail: The tissues pulldown menu controls the amount of cell cycle data displayed. By default, only the median values for selected cell cycle phases are shown. To display the value of all individual experimental replicates of all phases, select the all 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

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